←Back to structures

KR560069.1__AKO61721.1__X__00169

Bact-Vir

KR560069.1__AKO61721.1__X__00169

Identity

Accession:
KR560069 ↗
Kingdom:
phage

Quality

76.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Menderavirus› Stenotrophomonas_phage_IME-SM1

TaxID: 1654717

Cluster

Singleton — not in a non-trivial cluster

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 1-71
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1p32B00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.77 53.0 3.98e-01 71.8% 73.7%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 65.0 5.55e-01 100.0% 67.9%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 64.0 5.47e-01 100.0% 66.1%
4ie5A01 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.68 52.0 3.44e-01 80.3% 23.9%
4xhpA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.65 46.0 3.47e-01 94.4% 31.4%
2wpvE00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.63 33.0 2.22e-01 88.7% 12.9%
3sfvB01 3.30.450.390 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.63 53.0 4.25e-01 94.4% 95.1%
6n6qD00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.62 55.0 3.38e-01 100.0% 30.0%
7c2xA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.62 49.0 3.31e-01 87.3% 100.0%
3oduB01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.61 52.0 3.41e-01 100.0% 23.5%
7sf8A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.61 52.0 3.48e-01 93.0% 26.6%
5ttjA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.61 45.0 3.20e-01 78.9% 98.6%
1sfxB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 46.0 4.04e-01 83.1% 95.2%
2hc8A00 2.70.150.10 Mainly Beta › Distorted Sandwich › Calcium-transporting ATPase, cytoplasmic transduction domain A › Calcium-transporting ATPase, cytoplasmic transduction domain A 0.58 40.0 3.44e-01 71.8% 75.2%
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 50.0 4.60e-01 100.0% 75.5%
1vx7X00 3.30.1360.210 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.57 39.0 3.54e-01 71.8% 67.0%
4e1oA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 37.0 3.32e-01 70.4% 88.8%
4bgpA01 1.20.142.20 Mainly Alpha › Up-down Bundle › Poly(ADP-ribose) Polymerase; domain 1 › 0.54 45.0 3.75e-01 93.0% 59.1%
3mfqA01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.54 39.0 3.17e-01 77.5% 87.2%
2kx2A00 3.30.780.30 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › 0.53 40.0 3.63e-01 80.3% 61.5%
3qthB00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.53 43.0 3.31e-01 90.1% 81.1%
1pjqA02 3.30.160.110 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Sirohaem synthase, central domain 0.53 27.0 3.65e-01 91.5% 97.2%
2vsgA02 1.10.470.10 Mainly Alpha › Orthogonal Bundle › Variant Surface Glycoprotein, subunit A; domain 2 › Variant Surface Glycoprotein, subunit A, domain 2 0.53 42.0 3.34e-01 91.5% 47.5%
3g1nA02 3.30.2160.10 Alpha Beta › 2-Layer Sandwich › Hect, E3 ligase catalytic domain › Hect, E3 ligase catalytic domain 0.51 38.0 3.66e-01 78.9% 87.5%
1go4A00 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.51 43.0 3.10e-01 91.5% 51.0%
6nifA01 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.51 40.0 2.90e-01 85.9% 46.6%
3hh8A01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.51 39.0 3.16e-01 84.5% 87.9%
4nzrM03 3.30.110.180 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › 0.50 32.0 2.72e-01 87.3% 37.4%
ECOD (71)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3236563 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.87 56.0 4.54e-01 80.3% 37.6%
4385210 633.21.1.18 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CASP_dom 0.73 56.0 4.00e-01 80.3% 65.4%
4408503 192.2.1.43 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › TraD_N 0.71 55.0 4.37e-01 81.7% 52.6%
3413217 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.71 66.0 5.52e-01 100.0% 62.6%
3296120 3922.1.1.126 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › XH 0.71 41.0 3.68e-01 84.5% 41.0%
3921728 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.71 54.0 4.52e-01 80.3% 50.4%
3197800 221.13.1.2 ↗ a+b two layers › beta-Grasp › Mitochondrial calcium uniporter N-terminal domain › Mitochondrial calcium uniporter N-terminal domain › RRG1_C 0.70 54.0 4.00e-01 80.3% 75.2%
4236657 633.21.1.18 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CASP_dom 0.70 55.0 4.20e-01 83.1% 72.9%
3392569 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.70 65.0 5.28e-01 100.0% 56.8%
1000517 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.69 65.0 5.65e-01 100.0% 71.3%
3614763 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.69 62.0 5.13e-01 100.0% 57.5%
3394225 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.69 64.0 5.35e-01 100.0% 62.6%
3859550 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.69 65.0 5.30e-01 100.0% 60.0%
3493963 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.69 64.0 5.62e-01 100.0% 71.0%
60305 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.69 64.0 5.52e-01 100.0% 67.9%
3637098 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.69 63.0 5.06e-01 100.0% 54.1%
3550136 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.69 64.0 5.35e-01 100.0% 62.6%
3485296 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.69 64.0 5.52e-01 100.0% 68.6%
5028061 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 63.0 5.76e-01 100.0% 77.8%
5006841 103.4.1.0 ↗ alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein 0.68 55.0 4.42e-01 85.9% 83.8%
3579472 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 63.0 5.05e-01 100.0% 55.4%
4271212 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 63.0 5.14e-01 100.0% 58.5%
3234976 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 63.0 5.37e-01 100.0% 65.5%
4259368 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 63.0 5.18e-01 100.0% 60.0%
3690513 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 64.0 5.02e-01 100.0% 54.1%
3593339 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.68 63.0 5.26e-01 100.0% 62.6%
3712081 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 63.0 5.34e-01 100.0% 65.5%
4017372 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.67 63.0 5.27e-01 100.0% 62.6%
4662222 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.67 62.0 5.12e-01 100.0% 60.8%
4565985 5051.1.1.3 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › SSF 0.67 60.0 3.60e-01 100.0% 43.5%
3675304 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.67 62.0 5.11e-01 100.0% 60.0%
4224821 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.67 61.0 5.15e-01 100.0% 62.6%
3781291 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.67 62.0 5.43e-01 100.0% 76.0%
4457710 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 62.0 5.10e-01 100.0% 60.8%
3202986 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 62.0 5.00e-01 100.0% 57.6%
3787269 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 61.0 5.20e-01 100.0% 65.5%
3228583 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 61.0 5.14e-01 100.0% 62.6%
4977598 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 60.0 5.17e-01 100.0% 65.5%
3828336 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 62.0 5.17e-01 100.0% 63.2%
3594965 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 61.0 4.78e-01 100.0% 51.4%
4381440 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 60.0 5.08e-01 100.0% 62.6%
4681355 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 61.0 5.02e-01 100.0% 60.0%
3586018 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.66 61.0 4.77e-01 100.0% 51.4%
4940192 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.65 59.0 5.00e-01 100.0% 61.4%
5036014 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.65 59.0 5.32e-01 100.0% 73.7%
4666900 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.65 60.0 4.88e-01 100.0% 57.6%
4588825 589.1.1.20 ↗ alpha arrays › Triger factor/SurA peptide-binding domain-like › Triger factor/SurA peptide-binding domain-like › Porin chaperone SurA, peptide-binding domain › TraD_N 0.65 49.0 4.05e-01 81.7% 56.9%
3512585 5010.1.1.5 ↗ extended segments › Bacterial aa3 type cytochrome c oxidase subunit IV › Bacterial aa3 type cytochrome c oxidase subunit IV › Bacterial aa3 type cytochrome c oxidase subunit IV › TraD_N 0.64 49.0 4.22e-01 81.7% 64.3%
5029669 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.64 58.0 4.86e-01 100.0% 59.2%
5035493 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.64 59.0 5.13e-01 100.0% 68.6%
4112182 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.63 58.0 4.83e-01 100.0% 61.0%
3919851 109.4.1.335 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SEN1_N 0.63 47.0 2.80e-01 77.5% 15.2%
3935332 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.63 57.0 4.64e-01 100.0% 55.4%
4995244 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.63 57.0 4.91e-01 100.0% 64.5%
3749051 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.63 57.0 3.81e-01 100.0% 33.1%
3965667 109.4.1.520 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HemY_N 0.62 53.0 3.32e-01 100.0% 16.5%
4181293 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.62 56.0 4.82e-01 100.0% 65.5%
5041715 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.60 55.0 4.74e-01 100.0% 67.3%
3761098 4070.1.1.0 ↗ alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like 0.60 54.0 3.97e-01 97.2% 39.4%
4215095 604.39.1.0 ↗ alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters 0.60 54.0 3.36e-01 95.8% 30.6%
5062471 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.59 52.0 4.53e-01 100.0% 65.5%
4080548 223.1.1.176 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › KaiB 0.59 46.0 3.83e-01 83.1% 77.5%
3790018 3343.1.1.2 ↗ alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal,GCP_N_terminal 0.59 54.0 3.11e-01 100.0% 14.2%
3887088 4070.1.1.0 ↗ alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like 0.58 52.0 3.82e-01 100.0% 38.4%
3423625 109.4.1.1371 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, Eplus_motif, E_motif 0.57 35.0 2.06e-01 71.8% 7.7%
3737988 109.4.1.1316 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Suf, HAT_PRP39_N, HAT_PRP39_C 0.57 49.0 2.92e-01 100.0% 18.3%
5074130 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.55 50.0 3.37e-01 100.0% 71.8%
4620055 604.39.1.0 ↗ alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters 0.54 45.0 3.20e-01 95.8% 51.2%
3941035 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.52 39.0 2.84e-01 84.5% 87.0%
3424667 375.1.1.227 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › XH 0.51 40.0 3.66e-01 85.9% 98.9%
3367891 109.4.1.1272 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, E_motif 0.50 34.0 2.34e-01 71.8% 52.2%
D2 medium residues 88-143
PDB
Domain cluster: rep: NC_048804.1__YP_009851130.1__HWC60_gp073__00073__D157-203
D3 medium residues 144-214
PDB