←Back to structures

HQ634156.1__AGH32017.1__VPIG_00160__00159

Bact-Vir

HQ634156.1__AGH32017.1__VPIG_00160__00159

Identity

Accession:
HQ634156 ↗
Kingdom:
phage

Quality

83.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_PWH3a-P1

TaxID: 754058

Cluster

View cluster (5 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 18-102
PDB
Domain cluster: rep: OP056089.1__UYD72102.1__X__00002__D5-102
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07463.17 best NUMOD4 43.0 5.80e-11 50.6% 83.7%
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM01 3.90.75.20 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › 0.91 87.0 7.92e-01 100.0% 83.0%
1a73A00 3.90.75.10 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A 0.63 54.0 4.43e-01 96.5% 67.9%
6ruiB04 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.61 43.0 3.39e-01 74.1% 78.0%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.60 34.0 3.87e-01 70.6% 72.3%
3c4sA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.57 29.0 3.44e-01 94.1% 71.9%
3o8oF01 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 40.0 2.97e-01 75.3% 52.9%
2rjqA02 3.40.1620.60 Alpha Beta › 3-Layer(aba) Sandwich › YefM-like fold › 0.55 29.0 3.09e-01 77.6% 56.2%
5umbA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 48.0 3.81e-01 100.0% 68.0%
1vq8Q00 2.30.30.70 Mainly Beta › Roll › SH3 type barrels. › Ribosomal protein L21 0.54 32.0 3.11e-01 94.1% 52.6%
3zleA03 2.10.70.70 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.54 25.0 3.31e-01 83.5% 89.7%
1xkiA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 38.0 3.44e-01 78.8% 82.8%
2i2lA01 2.10.70.50 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.51 29.0 3.44e-01 78.8% 90.4%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3586841 378.1.1.7 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › NUMOD4,HNH_3 0.92 87.0 7.67e-01 98.8% 87.0%
8233 378.1.1.6 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › zf-His_Me_endon 0.63 54.0 4.43e-01 96.5% 67.9%
89916 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.63 54.0 4.43e-01 96.5% 67.9%
3881962 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.62 43.0 3.34e-01 71.8% 73.5%
5024226 375.1.1.83 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-TFIIB 0.61 29.0 3.67e-01 90.6% 80.0%
3366726 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.59 42.0 3.29e-01 76.5% 83.0%
4958343 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.58 39.0 3.85e-01 83.5% 64.4%
3258369 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 27.0 3.44e-01 78.8% 86.8%
3313424 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.57 51.0 4.01e-01 100.0% 81.7%
3595871 511.1.1.0 ↗ beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.57 50.0 3.42e-01 100.0% 46.9%
3307718 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.55 45.0 4.01e-01 88.2% 81.7%
5050368 4.1.1.14 ↗ beta barrels › SH3 › SH3 › SH3 › Ribosomal_L21e 0.54 32.0 3.09e-01 94.1% 52.0%
3822364 3270.1.1.1 ↗ a+b two layers › a+b domain in heme oxygenase › a+b domain in heme oxygenase › a+b domain in heme oxygenase › DUF2470 0.53 36.0 3.64e-01 95.3% 70.6%
5028212 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.52 38.0 3.17e-01 75.3% 67.6%
3591046 2002.3.1.2 ↗ a/b barrels › TIM beta/alpha-barrel › Glycoside hydrolase/deacetylase › Glycoside hydrolase/deacetylase › Polysacc_deac_1 0.52 43.0 2.96e-01 92.9% 56.2%
3572056 5.1.4.394 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_FAM234A_B 0.52 42.0 2.65e-01 89.4% 21.7%
5037381 375.1.1.19 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RNA_POL_M_15KD 0.51 28.0 3.40e-01 78.8% 88.0%
4031789 4959.1.1.0 ↗ a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit 0.51 33.0 3.79e-01 90.6% 93.3%
3370517 109.1.1.6 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C_2 0.51 37.0 3.14e-01 80.0% 72.5%
3346613 3270.1.1.1 ↗ a+b two layers › a+b domain in heme oxygenase › a+b domain in heme oxygenase › a+b domain in heme oxygenase › DUF2470 0.50 35.0 3.47e-01 96.5% 68.9%
D2 high residues 118-231
PDB
Domain cluster: rep: OM868075.1__UPT53026.1__X__00089__D7-115
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13392.13 best HNH_3 49.5 3.50e-13 31.6% 78.3%
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM01 3.90.75.20 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › 0.79 58.0 6.04e-01 96.5% 81.1%
3kxtA00 2.30.30.610 Mainly Beta › Roll › SH3 type barrels. › Chromatin protein Cren7 0.62 28.0 3.84e-01 94.7% 85.7%
5o99A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.59 23.0 2.99e-01 78.1% 60.0%
3vwoA02 2.10.70.40 Mainly Beta › Ribbon › Complement Module; domain 1 › peptidoglycan hydrolase 0.55 18.0 2.68e-01 84.2% 62.7%
1a73A00 3.90.75.10 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A 0.52 47.0 4.17e-01 98.2% 69.1%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3965202 378.1.1.19 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH_3 0.91 76.0 7.76e-01 94.7% 89.1%
3586841 378.1.1.7 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › NUMOD4,HNH_3 0.71 58.0 5.88e-01 96.5% 86.1%
3467905 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.63 27.0 3.69e-01 91.2% 80.0%
4618633 4.26.1.1 ↗ beta barrels › SH3 › Chromatin protein Cren7 › Chromatin protein Cren7 › Cren7 0.62 28.0 3.83e-01 94.7% 83.1%
8233 378.1.1.6 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › zf-His_Me_endon 0.52 47.0 4.17e-01 98.2% 69.1%
D3 high residues 237-334
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mgpA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.58 43.0 4.02e-01 77.6% 72.7%
3nyiA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.58 42.0 3.80e-01 77.6% 72.3%
5h8yD02 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.54 43.0 3.51e-01 87.8% 98.5%
2dt8A02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.54 39.0 3.62e-01 76.5% 73.8%
2dmyA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.53 37.0 3.73e-01 88.8% 72.2%
1el6A03 3.90.1160.10 Alpha Beta › Alpha-Beta Complex › Baseplate Structural Protein Gp11; Chain: A, domain 3 › Baseplate structural protein gp11, finger domain 0.53 37.0 3.59e-01 75.5% 65.1%
3venA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 38.0 2.89e-01 75.5% 87.7%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3813458 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.89 45.0 6.49e-01 82.7% 100.0%
3468885 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.80 58.0 6.45e-01 74.5% 92.5%
3467141 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.75 62.0 5.93e-01 85.7% 80.0%
3440839 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.74 60.0 6.02e-01 85.7% 94.0%
3331331 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.74 55.0 5.55e-01 77.6% 89.0%
3334492 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.73 54.0 5.97e-01 79.6% 92.5%
3827127 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.71 56.0 5.72e-01 83.7% 83.2%
3651077 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.71 48.0 5.66e-01 70.4% 100.0%
3370971 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.71 55.0 5.75e-01 80.6% 92.2%
3333577 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.71 59.0 6.05e-01 86.7% 91.6%
3327654 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.70 52.0 5.91e-01 82.7% 100.0%
3299337 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.68 56.0 5.60e-01 84.7% 88.8%
3664743 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.68 56.0 5.76e-01 86.7% 91.6%
3299580 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.66 38.0 4.42e-01 100.0% 83.1%
3657923 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.66 56.0 5.68e-01 87.8% 90.5%
3481102 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.62 38.0 3.50e-01 99.0% 46.4%
2324004 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.61 54.0 4.89e-01 95.9% 96.2%
3660311 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.61 36.0 3.97e-01 98.0% 72.5%
3853197 101.1.10.1 ↗ alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N 0.61 42.0 3.49e-01 71.4% 70.2%
3299579 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.59 37.0 4.26e-01 100.0% 88.6%
4944129 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.58 42.0 3.83e-01 75.5% 73.8%
2162577 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.57 41.0 3.72e-01 75.5% 70.1%
4134161 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.57 42.0 3.78e-01 77.6% 75.6%
4944239 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.56 40.0 3.69e-01 75.5% 73.8%
1936872 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.55 39.0 3.60e-01 74.5% 72.7%
3319893 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.54 38.0 3.84e-01 98.0% 72.0%
4946414 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.54 39.0 3.68e-01 76.5% 76.4%
3481288 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 39.0 3.73e-01 82.7% 67.0%
3213585 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 38.0 3.11e-01 77.6% 41.5%
5059595 213.1.1.21 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › LPG_synthase_C 0.52 40.0 3.71e-01 84.7% 82.3%
4503485 219.1.1.111 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core, Rad4 0.51 44.0 3.16e-01 100.0% 64.0%