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MK416015.1__QBP07934.1__X__00016

Bact-Vir

MK416015.1__QBP07934.1__X__00016

Identity

Accession:
MK416015 ↗
Kingdom:
phage

Quality

91.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Peduoviridae› Reipivirus› Klebsiella_phage_ST16-OXA48phi5.4

TaxID: 2510483

Cluster

View cluster (2 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 6-60_165-242
PDB
Domain cluster: rep: CAKLQF020000006.1__CAH1079955.1__SAMEA5780031_01448__00090__D4-139
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3jscA00 2.30.30.110 Mainly Beta › Roll › SH3 type barrels. › 0.78 53.0 6.16e-01 93.2% 95.8%
5hk0B00 2.30.30.110 Mainly Beta › Roll › SH3 type barrels. › 0.77 59.0 6.53e-01 95.5% 97.2%
1ne8A00 2.30.30.110 Mainly Beta › Roll › SH3 type barrels. › 0.74 59.0 6.33e-01 95.5% 94.8%
1ub4A00 2.30.30.110 Mainly Beta › Roll › SH3 type barrels. › 0.74 53.0 5.99e-01 95.5% 95.1%
1ib8A02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.64 31.0 4.12e-01 82.0% 89.6%
2lccA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.60 29.0 3.72e-01 80.5% 78.9%
4rmoA00 3.10.129.130 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › 0.60 53.0 5.01e-01 93.2% 83.1%
3m9qA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.60 31.0 4.04e-01 81.2% 91.7%
7afrX02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.59 27.0 3.79e-01 81.2% 93.3%
6vilA01 2.30.30.490 Mainly Beta › Roll › SH3 type barrels. › Bromo adjacent homology (BAH) domain 0.58 36.0 3.57e-01 85.0% 57.9%
5zwzA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.57 28.0 3.74e-01 79.7% 87.1%
1ts9A00 2.30.30.210 Mainly Beta › Roll › SH3 type barrels. › Ribonuclease P/MRP, subunit p29 0.56 28.0 3.23e-01 86.5% 64.3%
4atoA00 3.10.129.130 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › 0.54 47.0 4.37e-01 93.2% 78.0%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1952922 4.1.1.30 ↗ beta barrels › SH3 › SH3 › SH3 › PemK_toxin 0.79 61.0 6.69e-01 95.5% 97.2%
3290347 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.76 53.0 6.17e-01 94.0% 96.9%
3952707 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.73 63.0 6.37e-01 100.0% 91.5%
5013823 4.1.1.30 ↗ beta barrels › SH3 › SH3 › SH3 › PemK_toxin 0.68 62.0 6.29e-01 94.7% 100.0%
3595169 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 35.0 4.74e-01 82.0% 97.1%
3502388 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.65 29.0 3.80e-01 82.7% 73.3%
4995699 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.65 30.0 3.99e-01 82.7% 81.4%
3761318 4.1.1.253 ↗ beta barrels › SH3 › SH3 › SH3 › DUF4537 0.62 32.0 4.15e-01 82.0% 91.4%
3774692 4.1.1.31 ↗ beta barrels › SH3 › SH3 › SH3 › Spin-Ssty 0.62 35.0 4.42e-01 88.0% 92.5%
1688342 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 53.0 5.05e-01 94.0% 83.2%
3806777 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.60 32.0 4.14e-01 82.7% 90.7%
2410381 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.60 33.0 4.17e-01 83.5% 89.9%
3481770 4.1.1.220 ↗ beta barrels › SH3 › SH3 › SH3 › BAHCC1-like_Tudor 0.59 30.0 3.76e-01 84.2% 81.2%
3357709 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.58 33.0 3.98e-01 82.7% 84.7%
4132516 4.1.1.253 ↗ beta barrels › SH3 › SH3 › SH3 › DUF4537 0.58 31.0 3.73e-01 82.7% 81.2%
3826751 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.58 30.0 3.79e-01 82.7% 83.7%
3356605 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.57 34.0 4.01e-01 81.2% 86.7%
4466506 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 32.0 4.10e-01 86.5% 100.0%
3675653 4.1.1.239 ↗ beta barrels › SH3 › SH3 › SH3 › SH3-B_UBE2O 0.55 31.0 3.98e-01 82.7% 97.3%
3884661 4.1.1.382 ↗ beta barrels › SH3 › SH3 › SH3 › PF31078 0.53 35.0 3.76e-01 94.0% 79.1%
4963445 4.1.1.162 ↗ beta barrels › SH3 › SH3 › SH3 › DUF502 0.52 30.0 3.65e-01 85.7% 88.2%
4377781 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.52 32.0 3.87e-01 89.5% 100.0%
D2 high residues 63-161
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3u8vA00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.74 39.0 4.23e-01 81.8% 61.4%
3i9wA00 1.20.58.920 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 53.0 3.88e-01 78.8% 59.6%
1ki1B01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.67 50.0 4.01e-01 78.8% 72.4%
1v4aA03 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.66 49.0 4.26e-01 78.8% 71.2%
2q00B00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.63 48.0 4.49e-01 80.8% 70.5%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.63 38.0 4.38e-01 77.8% 84.5%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.62 47.0 4.49e-01 78.8% 97.4%
1y4cA03 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.61 41.0 3.96e-01 85.9% 61.1%
2z0qA01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.60 42.0 3.47e-01 74.7% 82.4%
1jalA03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.59 45.0 4.96e-01 92.9% 98.8%
3m7gA02 1.10.8.1010 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.59 43.0 4.47e-01 85.9% 80.0%
1xzpA02 1.20.120.430 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › tRNA modification GTPase MnmE domain 2 0.59 44.0 3.73e-01 87.9% 47.6%
4biuE01 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.59 37.0 3.79e-01 79.8% 64.3%
1xwmA00 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.58 43.0 3.46e-01 79.8% 63.2%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.58 38.0 4.07e-01 79.8% 77.6%
6jitB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.57 42.0 3.75e-01 75.8% 96.4%
3ggyA00 1.20.1260.60 Mainly Alpha › Up-down Bundle › Ferritin › Vacuolar protein sorting-associated protein Ist1 0.57 51.0 4.11e-01 97.0% 69.4%
2gd5A00 6.10.140.1230 Special › Helix non-globular › Helix Hairpins › 0.56 50.0 4.45e-01 98.0% 87.3%
1b0bA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.56 39.0 3.47e-01 70.7% 70.9%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.56 41.0 4.35e-01 76.8% 87.2%
1hw1A02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.54 40.0 3.49e-01 77.8% 56.3%
2ke4A00 6.10.140.470 Special › Helix non-globular › Helix Hairpins › 0.54 40.0 4.05e-01 77.8% 81.6%
1lm3B00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.53 37.0 3.66e-01 82.8% 67.9%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.53 38.0 4.13e-01 73.7% 91.3%
3frrA00 1.20.1260.60 Mainly Alpha › Up-down Bundle › Ferritin › Vacuolar protein sorting-associated protein Ist1 0.53 46.0 3.82e-01 100.0% 70.4%
4dxwA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 46.0 4.48e-01 100.0% 98.2%
8etcb01 1.20.120.1190 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 42.0 3.74e-01 87.9% 68.5%
1egdA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.52 46.0 4.13e-01 99.0% 88.7%
3na7A00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 39.0 2.97e-01 79.8% 33.8%
4dllB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.52 35.0 3.25e-01 70.7% 74.6%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.52 38.0 3.76e-01 79.8% 72.0%
2qkwA00 1.20.1270.140 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AvrPto 0.51 40.0 4.00e-01 88.9% 83.2%
4ioeA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.51 34.0 3.64e-01 90.9% 79.3%
4ijjB00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.51 42.0 3.89e-01 91.9% 76.9%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.50 38.0 4.05e-01 83.8% 94.1%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3593935 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.70 41.0 3.66e-01 79.8% 41.5%
4941322 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.70 60.0 4.24e-01 93.9% 40.0%
4932401 3930.1.1.3 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical 0.69 59.0 5.43e-01 94.9% 93.8%
3942473 6164.1.1.4 ↗ alpha bundles › Bestrophin › Bestrophin › Bestrophin › Bestrophin_2 0.69 52.0 3.67e-01 79.8% 45.7%
3975852 192.8.1.466 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Caudo_TAP 0.68 43.0 5.17e-01 84.8% 98.5%
3979204 605.2.1.8 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Caudo_TAP 0.67 44.0 4.97e-01 85.9% 88.0%
5071165 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.67 50.0 4.41e-01 79.8% 96.7%
4950656 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.67 50.0 4.62e-01 81.8% 60.8%
4010637 3809.1.1.2 ↗ alpha bundles › Uncharacterized protein CV0426 › Uncharacterized protein CV0426 › Uncharacterized protein CV0426 › Caudo_TAP 0.66 45.0 5.17e-01 85.9% 97.1%
5041256 601.4.1.91 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › PF30769 0.66 44.0 4.39e-01 86.9% 64.8%
4009505 7079.1.1.1 ↗ a+b complex topology › Phage tail fiber assembly protein › Phage tail fiber assembly protein › Phage tail fiber assembly protein › Caudo_TAP 0.66 45.0 5.18e-01 85.9% 98.6%
4007897 3809.1.1.2 ↗ alpha bundles › Uncharacterized protein CV0426 › Uncharacterized protein CV0426 › Uncharacterized protein CV0426 › Caudo_TAP 0.66 45.0 5.18e-01 85.9% 98.6%
4938202 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.65 47.0 4.66e-01 80.8% 71.4%
3602540 601.7.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.64 49.0 4.42e-01 82.8% 59.3%
4977213 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.64 53.0 4.02e-01 92.9% 38.4%
4485926 601.7.1.58 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › PF27235 0.64 49.0 4.40e-01 83.8% 64.1%
4784166 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.63 37.0 4.34e-01 76.8% 82.9%
4010437 3809.1.1.2 ↗ alpha bundles › Uncharacterized protein CV0426 › Uncharacterized protein CV0426 › Uncharacterized protein CV0426 › Caudo_TAP 0.63 43.0 4.92e-01 84.8% 97.1%
4249009 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.61 52.0 4.87e-01 91.9% 90.8%
4964513 622.4.1.66 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › FxsA 0.60 45.0 4.59e-01 87.9% 82.1%
4927881 601.18.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 0.59 37.0 3.88e-01 85.9% 68.9%
4342483 1128.1.1.1 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.58 35.0 3.72e-01 92.9% 66.7%
4235156 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.58 48.0 4.56e-01 90.9% 94.2%
3993362 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.58 48.0 4.83e-01 89.9% 92.0%
4927087 601.18.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 0.57 37.0 3.78e-01 85.9% 67.4%
4545635 1189.1.1.1 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › Trypan_glycop 0.57 50.0 3.42e-01 100.0% 61.8%
154418 106.1.1.1 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Globin 0.56 40.0 3.57e-01 75.8% 99.3%
3791225 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.56 41.0 3.91e-01 88.9% 65.2%
3284257 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.56 49.0 4.25e-01 94.9% 93.3%
3508214 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.54 35.0 3.28e-01 100.0% 50.8%
3691510 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.53 36.0 3.55e-01 87.9% 64.8%
3659874 611.9.1.4 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.53 43.0 3.78e-01 87.9% 79.3%
3386454 601.18.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 0.53 35.0 3.49e-01 81.8% 66.0%
3473220 5086.1.1.209 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › LIN9_C 0.52 39.0 3.77e-01 78.8% 68.7%
4031283 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.52 39.0 3.39e-01 78.8% 72.0%
3379416 109.4.1.1130 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_BSK1_C 0.52 40.0 3.45e-01 85.9% 94.9%
3609087 1189.1.1.1 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › Trypan_glycop 0.51 42.0 2.91e-01 89.9% 65.0%
3219915 2485.1.1.49 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_12 0.51 35.0 2.98e-01 71.7% 60.0%
4076285 3755.1.1.12 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › CheZ 0.51 38.0 3.44e-01 79.8% 67.1%
4996728 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.51 43.0 4.17e-01 97.0% 96.5%