←Back to structures

NC_013597.1__YP_003344802.1__D11S_2229__00022

Bact-Vir

NC_013597.1__YP_003344802.1__D11S_2229__00022

Identity

Accession:
NC_013597 ↗
Kingdom:
phage

Quality

84.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Aggregatibacter_phage_S1249

TaxID: 683735

Cluster

View cluster (116 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 25-81
PDB
Domain cluster: rep: OP172633.1__WAX05116.1__AB434P2_00043__00038__D17-94
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23982.3 best XM1_gp53_minor_capsid 27.9 2.60e-06 100.0% 40.3%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6xgqb01 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.80 74.0 6.16e-01 100.0% 62.4%
1c5eA00 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.75 65.0 5.49e-01 100.0% 58.9%
8bveA03 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.74 66.0 6.09e-01 100.0% 98.6%
1g8lA04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.73 65.0 6.00e-01 100.0% 98.6%
6ethA04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.69 60.0 5.23e-01 100.0% 87.6%
3cp7B02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.62 45.0 3.74e-01 100.0% 42.9%
1b23P03 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 50.0 4.29e-01 100.0% 60.6%
2bhgA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.57 41.0 3.46e-01 100.0% 43.1%
1yu0A02 2.80.20.10 Mainly Beta › Trefoil › Tail fiber receptor-binding protein › Tail fiber receptor-binding protein 0.56 46.0 3.61e-01 100.0% 71.2%
1wxxA01 2.30.130.10 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › PUA domain 0.51 34.0 3.40e-01 100.0% 64.6%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5083816 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.86 79.0 7.31e-01 100.0% 90.0%
2559744 70.4.1.2 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.86 70.0 6.97e-01 100.0% 84.7%
5002644 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.85 77.0 7.01e-01 100.0% 93.3%
3981037 70.4.1.9 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement_2 0.80 68.0 6.90e-01 100.0% 96.4%
4963571 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.80 68.0 6.48e-01 100.0% 80.0%
2640772 70.4.1.1 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › HDPD 0.80 74.0 5.99e-01 100.0% 58.0%
4930420 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.80 67.0 6.25e-01 100.0% 74.3%
5022524 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.80 67.0 6.26e-01 100.0% 74.3%
5039270 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.79 65.0 6.60e-01 98.2% 90.9%
5007190 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.78 62.0 6.61e-01 96.5% 96.0%
5002645 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.76 67.0 6.68e-01 100.0% 94.9%
2808420 70.4.1.1 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › HDPD 0.73 63.0 5.12e-01 100.0% 51.4%
5030835 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.73 65.0 5.67e-01 100.0% 85.9%
5049149 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.72 65.0 5.95e-01 100.0% 97.3%
5075574 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.72 63.0 5.69e-01 100.0% 90.0%
2984229 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.72 64.0 5.78e-01 100.0% 89.7%
4956897 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.72 64.0 5.72e-01 100.0% 90.0%
2526359 70.4.1.2 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.71 59.0 5.89e-01 100.0% 90.0%
3513462 70.4.1.8 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement 0.71 63.0 6.19e-01 100.0% 93.3%
3945811 70.4.1.7 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › XM1_gp53_minor_capsid 0.71 63.0 6.19e-01 98.2% 93.3%
4960949 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 61.0 5.52e-01 100.0% 88.7%
4975116 70.1.1.0 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like 0.70 61.0 5.52e-01 100.0% 88.7%
4950136 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 61.0 5.56e-01 98.2% 93.3%
4933166 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 62.0 5.53e-01 100.0% 92.5%
3205316 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 61.0 5.27e-01 100.0% 91.1%
4982596 70.1.1.0 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like 0.68 60.0 5.65e-01 100.0% 97.1%
4070519 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.68 59.0 5.44e-01 100.0% 97.3%
4935036 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.68 60.0 5.58e-01 100.0% 91.8%
5011090 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.67 59.0 5.39e-01 98.2% 92.0%
3655832 7517.1.1.1 ↗ a/b three-layered sandwiches › Nucleoside hydrolase › Nucleoside hydrolase › Nucleoside hydrolase › IU_nuc_hydro 0.59 42.0 2.64e-01 78.9% 47.2%
4165709 1.1.7.19 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › GTP_EFTU_D2 0.57 49.0 4.08e-01 100.0% 54.3%
4163851 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.56 37.0 3.73e-01 89.5% 66.7%
1107991 4166.1.1.4 ↗ beta sandwiches › Lactophage receptor-binding protein N-terminal domain-like › Lactophage receptor-binding protein N-terminal domain-like › Lactophage receptor-binding protein N-terminal domain-like › mtd_2nd 0.56 46.0 3.81e-01 100.0% 89.7%
4280097 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.56 38.0 3.73e-01 89.5% 66.7%
3839016 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.54 37.0 3.61e-01 89.5% 63.1%
3781831 223.2.1.28 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Afi1 0.54 44.0 3.26e-01 100.0% 58.9%
3190266 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 40.0 2.56e-01 87.7% 44.7%
D2 high residues 87-148
PDB
Domain cluster: rep: CAKLQH020000012.1__CAH1086588.1__SAMEA5780036_01984__00028__D92-158
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23982.3 best XM1_gp53_minor_capsid 29.5 8.70e-07 98.4% 30.5%
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5gxuB01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.69 46.0 3.72e-01 100.0% 36.1%
5tr9A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 43.0 3.76e-01 100.0% 51.0%
1vwxM01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.59 41.0 3.73e-01 74.2% 90.6%
5i7pA02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.58 41.0 4.57e-01 100.0% 97.9%
3h41A02 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.58 40.0 3.93e-01 72.6% 97.1%
1ywuA00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.57 42.0 3.38e-01 100.0% 39.2%
4q63A00 2.40.10.430 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.57 39.0 3.46e-01 100.0% 48.4%
1ynjD03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.55 42.0 4.45e-01 100.0% 100.0%
2gpjA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.55 42.0 3.67e-01 100.0% 54.0%
1wu2A04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.53 47.0 4.37e-01 100.0% 90.9%
3nyqA01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.52 44.0 2.81e-01 100.0% 30.7%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.51 36.0 3.41e-01 100.0% 60.8%
3lnnA01 2.40.420.20 Mainly Beta › Beta Barrel › conserved putative lor/sdh protein from methanococcus maripaludis s2 fold › 0.51 36.0 3.23e-01 98.4% 51.6%
3iplB01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.50 43.0 2.72e-01 100.0% 30.5%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3513462 70.4.1.8 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement 0.79 67.0 6.86e-01 100.0% 96.7%
4583854 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.64 46.0 5.04e-01 98.4% 96.0%
4246480 1.1.5.25 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.62 45.0 3.96e-01 100.0% 50.5%
4319764 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.60 42.0 3.54e-01 100.0% 42.7%
3960060 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.59 42.0 3.01e-01 100.0% 25.4%
5041405 325.1.7.8 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › RnfC_N 0.53 45.0 4.42e-01 98.4% 87.1%
4016558 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.53 46.0 3.55e-01 100.0% 57.2%
3449852 75.1.1.1 ↗ beta barrels › Cyclophilin-like › Cyclophilin-like › Cyclophilin-like › Pro_isomerase 0.52 41.0 3.02e-01 91.9% 77.9%
3525543 11.1.1.991 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF28112 0.51 39.0 3.23e-01 100.0% 45.5%
4128441 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.50 39.0 3.96e-01 100.0% 93.3%