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MK291441.1__AZV00170.1__pben1_p13__00012

Bact-Vir

MK291441.1__AZV00170.1__pben1_p13__00012

Identity

Accession:
MK291441 ↗
Kingdom:
phage

Quality

86.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Paracoccus_phage_vB_PbeS_Pben1

TaxID: 2500567

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 8-67
PDB
Domain cluster: rep: JQ066768.1__AFA44883.1__RcapNL_00043__00043__D7-72
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF27127.1 best YfdP 51.4 1.80e-13 100.0% 75.3%
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2xefA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.70 54.0 3.35e-01 81.7% 15.6%
2ebfX01 3.10.670.10 Alpha Beta › Roll › Secreted effector protein ssei fold › Secreted effector protein ssei. 0.70 50.0 3.56e-01 81.7% 24.4%
2c42A03 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.68 48.0 3.29e-01 88.3% 21.2%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.67 55.0 4.37e-01 90.0% 81.5%
4wksC02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.66 44.0 4.08e-01 71.7% 54.7%
6nvxB02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.66 43.0 4.02e-01 71.7% 53.2%
7f79A01 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.65 47.0 3.55e-01 81.7% 56.6%
3oc9A00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.64 52.0 3.16e-01 91.7% 38.2%
2ek0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.64 49.0 4.33e-01 88.3% 56.7%
3w1hA01 3.90.1150.110 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.63 49.0 3.43e-01 86.7% 26.5%
3hm2A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.63 43.0 3.22e-01 75.0% 26.3%
3iabB01 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.62 47.0 4.02e-01 81.7% 50.5%
6canA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.62 46.0 2.93e-01 80.0% 25.5%
7zqiA01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.59 45.0 3.27e-01 85.0% 78.1%
1pu1A00 3.30.300.100 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like 0.58 47.0 4.11e-01 88.3% 78.0%
1novA00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.58 43.0 2.77e-01 81.7% 80.3%
4iiqC02 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.58 44.0 3.21e-01 83.3% 77.5%
3fruA01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.58 47.0 3.55e-01 100.0% 44.6%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 33.0 2.28e-01 81.7% 16.7%
1gaxA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.57 51.0 3.21e-01 100.0% 79.9%
1f8vC00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.57 42.0 2.73e-01 81.7% 81.0%
1xttB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 43.0 2.91e-01 80.0% 88.5%
4eo0A00 3.30.110.160 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › 0.56 46.0 3.91e-01 95.0% 59.4%
3lxrF00 1.10.4120.20 Mainly Alpha › Orthogonal Bundle › SopE-like GEF fold › 0.55 47.0 3.30e-01 91.7% 66.9%
1bd3A00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 42.0 2.80e-01 80.0% 81.7%
1fm2B03 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.55 37.0 3.66e-01 76.7% 63.6%
5cw3C01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.55 42.0 3.13e-01 80.0% 35.4%
1se8A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 38.0 3.19e-01 93.3% 40.5%
1dpgA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.54 46.0 2.95e-01 98.3% 56.6%
5n6lA01 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.54 42.0 2.84e-01 88.3% 87.4%
4zg5A00 3.40.1210.10 Alpha Beta › 3-Layer(aba) Sandwich › Stationary-phase Survival Protein Sure Homolog; Chain: A, › Survival protein SurE-like phosphatase/nucleotidase 0.54 41.0 2.71e-01 81.7% 68.4%
2onfA01 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.53 46.0 3.58e-01 96.7% 73.9%
2d42A02 3.10.450.380 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 38.0 3.72e-01 75.0% 80.0%
1dt9A01 3.30.960.10 Alpha Beta › 2-Layer Sandwich › Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A › eRF1 domain 1 0.53 44.0 3.82e-01 100.0% 81.9%
3icsA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 44.0 2.97e-01 98.3% 42.2%
4gs5A02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.53 43.0 3.72e-01 96.7% 58.1%
1vwxP00 3.90.470.10 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › Ribosomal protein L22/L17 0.53 47.0 3.49e-01 100.0% 77.8%
1yk9A00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.53 40.0 2.91e-01 85.0% 35.3%
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 45.0 2.94e-01 100.0% 83.5%
1pfoA02 3.30.1040.20 Alpha Beta › 2-Layer Sandwich › Carboxypeptidase Inhibitor; Chain A › 0.52 37.0 3.82e-01 88.3% 86.8%
4fo0A03 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.52 42.0 3.08e-01 88.3% 85.0%
3vpyA00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.52 41.0 3.25e-01 95.0% 54.5%
1aroP05 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.51 45.0 3.08e-01 100.0% 48.8%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3636298 5001.1.1.6 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Bac_rhodopsin 0.71 58.0 3.85e-01 90.0% 85.0%
3714030 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.70 49.0 2.71e-01 73.3% 51.5%
3964912 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.68 43.0 4.11e-01 93.3% 52.7%
4309637 1036.1.1.1 ↗ a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.68 47.0 4.21e-01 90.0% 52.4%
4883006 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.63 44.0 2.99e-01 73.3% 38.9%
3207615 5051.1.1.10 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › AA_permease_2 0.62 50.0 2.97e-01 88.3% 64.3%
5037829 304.5.1.3 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › CutA1 0.62 45.0 3.81e-01 80.0% 47.0%
3956484 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.61 48.0 3.95e-01 90.0% 51.7%
5030848 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.61 44.0 3.32e-01 76.7% 34.5%
5012554 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.61 41.0 2.85e-01 76.7% 20.0%
4836497 233.1.1.1 ↗ a+b two layers › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC_I 0.61 46.0 3.35e-01 83.3% 77.1%
3986530 330.1.1.33 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › SF0329 0.61 42.0 3.25e-01 100.0% 35.0%
4233442 304.4.1.54 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Amnionless 0.61 48.0 3.91e-01 90.0% 47.5%
4378403 210.1.2.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › Penicil_amidase 0.60 53.0 2.97e-01 100.0% 84.7%
4202672 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.60 45.0 3.10e-01 85.0% 49.8%
4233683 171.1.1.1 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like › Ribonuclease_3 0.60 48.0 3.35e-01 91.7% 77.7%
3675745 328.1.1.1 ↗ a+b two layers › IF3-like › AlbA-like › AlbA-like › Alba 0.59 48.0 4.55e-01 90.0% 80.8%
4116373 5085.1.1.1 ↗ a+b duplicates or obligate multimers › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › OEP 0.59 52.0 3.12e-01 100.0% 52.7%
4891081 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.57 40.0 3.00e-01 73.3% 34.0%
4028937 109.4.1.1255 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N, Cnd1 0.57 44.0 2.49e-01 83.3% 9.3%
4004108 273.1.1.1 ↗ a+b three layers › PR-1-like › PR-1-like › PR-1-like › CAP 0.57 49.0 3.27e-01 100.0% 51.2%
3997559 273.1.1.1 ↗ a+b three layers › PR-1-like › PR-1-like › PR-1-like › CAP 0.56 48.0 3.25e-01 98.3% 29.6%
3943661 304.5.1.13 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF3574 0.56 41.0 3.54e-01 95.0% 48.0%
None — 0.56 44.0 2.69e-01 86.7% 20.1%
4882343 2003.1.1.59 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NAD_binding_5 0.56 44.0 2.76e-01 86.7% 23.9%
4160692 171.1.1.1 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like › Ribonuclease_3 0.56 44.0 3.06e-01 90.0% 75.6%
3214850 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.56 47.0 2.91e-01 95.0% 26.0%
4013407 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.55 45.0 3.01e-01 100.0% 85.9%
2507516 210.1.2.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › Penicil_amidase 0.55 46.0 2.76e-01 98.3% 28.9%
4399128 7581.1.1.30 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Thiolase_N, ketoacyl-synt, Thiolase_C 0.55 48.0 2.98e-01 100.0% 51.1%
3983446 101.1.2.84 ↗ alpha arrays › HTH › HTH › winged helix domain › CaiF_GrlA 0.55 37.0 3.25e-01 86.7% 43.0%
4487061 328.8.1.1 ↗ a+b two layers › IF3-like › Schlafen 8 › Schlafen 8 › SLFN_AlbA_2 0.55 41.0 3.15e-01 88.3% 34.1%
3838659 5085.1.1.0 ↗ a+b duplicates or obligate multimers › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.54 47.0 2.87e-01 100.0% 58.2%
3639274 261.1.1.1 ↗ a+b complex topology › Hect, E3 ligase catalytic domain › Hect, E3 ligase catalytic domain › Hect, E3 ligase catalytic domain › HECT 0.53 39.0 2.32e-01 80.0% 13.8%
3604748 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 44.0 3.13e-01 100.0% 79.1%
3942393 2004.1.1.173 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TrwB_AAD_bind 0.52 39.0 2.38e-01 83.3% 87.6%
4973231 304.48.1.20 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Thg1 0.52 46.0 3.03e-01 98.3% 46.3%
3475563 3926.1.1.2 ↗ alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › Vma22_CCDC115 0.52 43.0 3.07e-01 90.0% 82.1%
3603683 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.52 40.0 3.08e-01 88.3% 35.9%
5057424 177.1.1.0 ↗ alpha bundles › Phospholipase C/P1 nuclease › Phospholipase C/P1 nuclease › Phospholipase C/P1 nuclease 0.52 44.0 3.06e-01 98.3% 52.3%
3932950 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 42.0 2.71e-01 100.0% 21.1%
3874464 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.51 38.0 2.46e-01 86.7% 55.8%
3815772 109.4.1.1580 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT, HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N, HAT_PRP39_N, HAT_PRP39_C 0.51 41.0 2.37e-01 88.3% 8.8%
1569515 11.1.1.248 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › bMG6 0.50 41.0 3.65e-01 93.3% 95.6%
4452393 304.112.1.10 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain › Med13_N 0.50 41.0 3.56e-01 100.0% 71.4%