←Back to structures

KJ746502.1__AID18359.1__PPF1_46__00046

Bact-Vir

KJ746502.1__AID18359.1__PPF1_46__00046

Identity

Accession:
KJ746502 ↗
Kingdom:
phage

Quality

89.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_vB_RleM_PPF1

TaxID: 1498228

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 4-94
PDB
Domain cluster: rep: S2_012_000_R2_scaffold_0_prodigal-single.1__X__X__00667__D16-97
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3u12A00 2.30.29.180 Mainly Beta › Roll › PH-domain like › Ubiquitin carboxyl-terminal hydrolase 26/29/37, pleckstrin homology-like domain 0.60 42.0 4.05e-01 73.6% 73.1%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 43.0 3.95e-01 81.3% 90.9%
5mu3B00 3.40.50.12050 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 40.0 3.35e-01 75.8% 42.9%
4joiA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 39.0 3.45e-01 73.6% 100.0%
1p5tA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 40.0 3.86e-01 76.9% 74.5%
4bf3A00 2.30.31.50 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Borrelia outer surface protein E/F 0.53 37.0 3.33e-01 73.6% 66.2%
3oduB01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.53 43.0 3.05e-01 91.2% 28.9%
2crfA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 39.0 3.59e-01 80.2% 70.4%
2y3vD00 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.51 38.0 3.29e-01 80.2% 58.4%
3zl8A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.51 35.0 2.70e-01 71.4% 50.9%
4fr9A00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.50 34.0 3.01e-01 70.3% 90.8%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4963351 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 45.0 4.12e-01 73.6% 79.2%
4029381 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.62 47.0 3.83e-01 81.3% 88.3%
3719245 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.62 39.0 3.02e-01 79.1% 28.0%
3180758 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.61 37.0 3.03e-01 79.1% 31.8%
3788985 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 46.0 3.97e-01 81.3% 70.3%
4017732 220.1.1.202 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_FT_N 0.60 45.0 3.83e-01 79.1% 67.3%
3199763 220.1.1.202 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_FT_N 0.58 44.0 4.04e-01 81.3% 84.8%
3700838 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.58 44.0 4.00e-01 82.4% 83.1%
4598415 3926.1.1.1 ↗ alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.56 44.0 3.38e-01 83.5% 39.5%
4027836 220.1.1.13 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DCP1 0.56 43.0 3.70e-01 83.5% 56.0%
3925367 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 42.0 3.64e-01 82.4% 80.0%
3962103 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.56 42.0 4.05e-01 81.3% 69.5%
3273166 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 41.0 2.85e-01 79.1% 70.6%
3479960 5.1.4.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CNH 0.54 39.0 2.68e-01 76.9% 63.2%
3510425 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.54 40.0 3.42e-01 79.1% 79.4%
3219546 220.1.1.4 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Ran_BP1 0.54 44.0 3.77e-01 91.2% 63.3%
4307499 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.54 43.0 3.65e-01 84.6% 97.9%
4952130 3714.1.1.1 ↗ a+b two layers › Lon-like protease MtaLonC helical domain › Lon-like protease MtaLonC helical domain › Lon-like protease MtaLonC helical domain › LonC_helical 0.53 46.0 3.43e-01 96.7% 37.4%
3929344 3409.1.1.1 ↗ a+b duplicates or obligate multimers › Vacuolar protein sorting-associated protein 30 BARA domain › Vacuolar protein sorting-associated protein 30 BARA domain › Vacuolar protein sorting-associated protein 30 BARA domain › APG6 0.53 37.0 2.87e-01 91.2% 34.2%
3271052 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.53 39.0 3.30e-01 76.9% 61.4%
3895743 3615.1.1.7 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › CD20 0.52 47.0 3.70e-01 100.0% 91.1%
1179397 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.52 32.0 2.76e-01 80.2% 34.6%
4171807 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.52 46.0 3.78e-01 95.6% 99.4%
5008037 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 37.0 3.36e-01 74.7% 92.0%
4440404 4325.1.1.15 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › PF26354 0.51 38.0 3.45e-01 78.0% 91.7%
5078870 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.50 43.0 3.74e-01 93.4% 94.3%
4001931 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.50 35.0 3.15e-01 72.5% 83.7%
3196528 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.50 30.0 3.67e-01 73.6% 91.7%
D2 high residues 97-170
PDB
Domain cluster: rep: OR545055.1__WOZ55967.1__P44_00046__00046__D3-75
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 40.0 3.62e-01 77.0% 49.5%
2uuzB00 1.10.10.2020 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Host-nuclease inhibitor protein Gam 0.61 40.0 3.84e-01 100.0% 58.8%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.58 33.0 3.53e-01 77.0% 61.2%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.57 38.0 3.37e-01 77.0% 49.0%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.57 38.0 3.73e-01 77.0% 63.3%
3ccyA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 40.0 3.17e-01 79.7% 36.7%
2icwG01 1.20.120.390 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1 0.56 48.0 4.07e-01 100.0% 57.3%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.56 37.0 3.73e-01 85.1% 65.4%
6jlzA01 1.20.120.1070 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Translation initiation factor eIF-2B, N-terminal domain 0.54 37.0 3.32e-01 75.7% 50.0%
1quuA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 39.0 3.24e-01 77.0% 44.4%
1n5uA02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.53 48.0 4.48e-01 100.0% 85.6%
4ioeA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.52 36.0 3.48e-01 78.4% 62.1%
2owaA01 1.10.220.150 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Arf GTPase activating protein 0.52 45.0 3.86e-01 97.3% 81.7%
7wu8B01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.52 35.0 3.47e-01 90.5% 65.8%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 33.0 2.91e-01 73.0% 41.9%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.51 38.0 3.31e-01 77.0% 70.0%
7r0kB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.50 44.0 3.07e-01 100.0% 75.0%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5074957 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.64 49.0 5.10e-01 100.0% 87.1%
4646569 4994.1.1.1 ↗ alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507 0.64 40.0 3.64e-01 81.1% 49.5%
3719058 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.62 38.0 3.66e-01 75.7% 54.1%
4365458 3960.1.1.1 ↗ alpha arrays › Aminoglycoside adenyltransferase AadA C-terminal domain › Aminoglycoside adenyltransferase AadA C-terminal domain › Aminoglycoside adenyltransferase AadA C-terminal domain › AadA_C 0.61 52.0 4.67e-01 100.0% 78.7%
3286065 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.59 46.0 4.73e-01 100.0% 90.0%
3379886 604.12.1.85 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › 14-3-3 0.56 37.0 3.42e-01 77.0% 53.2%
3290948 3960.1.1.1 ↗ alpha arrays › Aminoglycoside adenyltransferase AadA C-terminal domain › Aminoglycoside adenyltransferase AadA C-terminal domain › Aminoglycoside adenyltransferase AadA C-terminal domain › AadA_C 0.56 47.0 4.31e-01 97.3% 80.0%
3516297 2484.1.1.21 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › BcrAD_BadFG 0.56 45.0 3.34e-01 90.5% 61.0%
55471 611.5.1.0 ↗ alpha bundles › N-cbl like › Superantigen MAM N-terminal domain › Superantigen MAM N-terminal domain 0.55 47.0 4.02e-01 100.0% 57.3%
3644387 601.1.2.81 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Serinc 0.55 48.0 3.87e-01 100.0% 49.3%
3407158 101.3.1.0 ↗ alpha arrays › HTH › XPC-binding domain › XPC-binding domain 0.54 41.0 3.67e-01 83.8% 100.0%
4886833 601.48.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › vWA2 C-terminal domain › vWA2 C-terminal domain › ArnB_C 0.53 40.0 3.78e-01 97.3% 64.9%
4955751 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.53 47.0 4.42e-01 100.0% 83.3%
3988025 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.53 38.0 3.35e-01 82.4% 50.9%
3415313 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 37.0 2.49e-01 77.0% 18.4%
3997786 4193.1.1.0 ↗ alpha arrays › RUN domain › RUN domain › RUN domain 0.51 43.0 3.44e-01 97.3% 58.7%
3596653 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.51 42.0 3.70e-01 97.3% 80.8%
1697185 532.2.1.3 ↗ alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains › TyeA 0.50 41.0 3.84e-01 91.9% 98.9%
4986013 4994.1.1.0 ↗ alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like 0.50 36.0 3.42e-01 74.3% 76.5%