←Back to structures

KX581096.3__AOT26814.1__pVa5_0045__00044

Bact-Vir

KX581096.3__AOT26814.1__pVa5_0045__00044

Identity

Accession:
KX581096 ↗
Kingdom:
phage

Quality

88.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_vB_VspP_pVa5_12Jun

TaxID: 2890992

Cluster

View cluster (35 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 2-162
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1hjrA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.76 67.0 6.76e-01 91.3% 98.7%
3thxB02 3.30.420.110 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › MutS, connector domain 0.70 55.0 5.70e-01 95.0% 86.8%
3hrgA02 3.30.420.260 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, C-terminal domain 0.68 42.0 4.95e-01 97.5% 86.8%
2derB01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.65 46.0 4.22e-01 91.3% 56.7%
4wnyA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.65 43.0 4.68e-01 88.8% 81.1%
4jc0A03 3.30.750.200 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.64 36.0 4.15e-01 80.7% 74.2%
3s3tA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.61 41.0 4.27e-01 88.8% 73.8%
2ap1A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 49.0 5.28e-01 90.7% 100.0%
8oqkA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 38.0 4.64e-01 86.3% 100.0%
2ivnA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 51.0 5.10e-01 93.2% 100.0%
2e2oA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 44.0 4.87e-01 96.9% 98.5%
1y1pA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 51.0 4.08e-01 100.0% 100.0%
1sazA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 48.0 4.67e-01 91.3% 85.8%
3i8oA01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.55 42.0 4.70e-01 81.4% 100.0%
2bd0A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 47.0 4.13e-01 90.7% 93.6%
5ywwA01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.54 37.0 4.32e-01 85.1% 97.4%
3fg9C01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.54 43.0 4.60e-01 93.8% 95.0%
3ucxA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 45.0 3.90e-01 91.3% 92.6%
2hqmA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 42.0 3.74e-01 82.6% 87.7%
1onfA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 42.0 3.90e-01 82.6% 88.2%
3idfA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 41.0 4.43e-01 95.0% 94.9%
4s1wB02 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.53 40.0 4.23e-01 96.9% 88.4%
2wk1A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 40.0 3.52e-01 78.9% 81.0%
2gm3A00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 41.0 4.26e-01 95.0% 86.9%
3hsiA01 3.30.870.10 Alpha Beta › 2-Layer Sandwich › Endonuclease; Chain A › Endonuclease Chain A 0.52 43.0 3.80e-01 95.7% 59.2%
6g80B01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 45.0 4.09e-01 94.4% 94.1%
1vsrA00 3.40.960.10 Alpha Beta › 3-Layer(aba) Sandwich › Endonuclease; Chain A › VSR Endonuclease 0.52 37.0 3.96e-01 83.2% 85.8%
1lvlA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 41.0 3.73e-01 82.6% 88.5%
3gdgA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 46.0 3.87e-01 95.7% 90.3%
4zd6C00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 45.0 4.09e-01 95.7% 95.5%
3tbfA02 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.52 40.0 4.18e-01 95.0% 87.9%
1gy8D02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 43.0 3.81e-01 90.1% 92.3%
6uh2A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 43.0 3.83e-01 91.3% 95.4%
4e19A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 38.0 4.19e-01 82.6% 94.7%
1w97L01 3.30.420.380 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.51 43.0 4.43e-01 91.3% 94.2%
1jhdA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.51 40.0 3.68e-01 92.5% 64.5%
2x9qB00 3.40.50.11710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cyclodipeptide synthase 0.51 45.0 4.09e-01 98.1% 80.2%
8a26A01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.50 43.0 3.60e-01 91.3% 99.3%
1k92A01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.50 39.0 3.95e-01 80.7% 92.5%
6ln3A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 42.0 3.93e-01 90.1% 98.0%
1fkwA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.50 42.0 3.32e-01 91.3% 93.4%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5082200 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.82 53.0 6.28e-01 88.2% 91.3%
5042784 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.80 55.0 6.40e-01 91.3% 95.0%
4991588 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.79 54.0 5.30e-01 90.1% 64.0%
4172297 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.79 69.0 6.72e-01 91.3% 94.8%
5063663 2484.1.1.144 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DEDD_Tnp_IS110 0.78 50.0 6.19e-01 90.1% 99.0%
4979556 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.77 67.0 6.00e-01 91.3% 93.5%
3589909 2484.1.1.144 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DEDD_Tnp_IS110 0.76 53.0 6.09e-01 90.7% 95.0%
4938348 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.75 67.0 6.66e-01 92.5% 97.0%
4979039 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.74 64.0 5.83e-01 91.3% 96.7%
4669382 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.72 64.0 6.34e-01 93.2% 98.2%
4423692 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.70 56.0 5.93e-01 92.5% 95.0%
5041441 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.69 44.0 4.53e-01 89.4% 66.5%
4533621 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.69 56.0 5.87e-01 91.3% 92.0%
4962880 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.68 60.0 5.32e-01 93.2% 87.6%
4984720 2484.1.1.333 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF1464 0.68 60.0 4.52e-01 95.0% 91.8%
4990645 2484.1.1.139 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF429 0.67 61.0 6.04e-01 95.0% 99.4%
5075582 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.66 58.0 5.09e-01 92.5% 91.7%
4949807 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.66 44.0 4.56e-01 89.4% 71.3%
4983835 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.65 41.0 4.47e-01 88.8% 74.8%
3603346 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.64 43.0 4.33e-01 88.8% 66.9%
5052045 7592.1.1.0 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains 0.64 50.0 4.69e-01 80.1% 79.5%
5064569 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.64 55.0 5.38e-01 91.3% 98.9%
4959883 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.63 43.0 4.49e-01 88.8% 74.3%
407730 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.63 41.0 4.33e-01 85.7% 72.2%
4951031 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.63 42.0 4.42e-01 87.6% 72.7%
3839224 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.63 41.0 4.41e-01 88.8% 76.3%
4623449 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.63 42.0 5.11e-01 96.3% 100.0%
4996735 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.63 54.0 5.21e-01 95.0% 81.1%
None — 0.63 44.0 3.94e-01 90.7% 52.8%
5061663 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.62 42.0 4.43e-01 89.4% 75.2%
4330193 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.62 38.0 4.69e-01 96.3% 98.0%
4229347 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.62 42.0 4.97e-01 98.8% 100.0%
4072319 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.62 42.0 4.99e-01 99.4% 100.0%
5048111 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.62 41.0 4.24e-01 88.8% 71.1%
3825814 2005.1.1.41 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.62 48.0 4.62e-01 82.0% 87.6%
4419955 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 38.0 4.73e-01 97.5% 100.0%
4661838 2484.1.1.48 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MutS_II 0.61 54.0 5.13e-01 94.4% 80.5%
4928314 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.60 40.0 4.25e-01 87.0% 75.2%
5025630 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.60 39.0 4.14e-01 88.8% 72.4%
4264624 2484.1.1.12 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Acetate_kinase 0.60 52.0 3.94e-01 91.9% 94.6%
3470605 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.60 42.0 4.34e-01 90.1% 76.0%
3953050 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.59 39.0 4.09e-01 87.6% 73.1%
4937064 2484.1.1.8 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.59 50.0 4.01e-01 90.1% 98.7%
3959532 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.57 40.0 3.92e-01 91.9% 65.7%
3603301 7592.1.1.6 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › Csa3_N 0.57 41.0 4.42e-01 89.4% 85.7%
3291241 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.56 37.0 3.82e-01 88.2% 70.0%
3685788 2003.1.6.6 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like › Misat_Tub_SegII+Tubulin_3 0.56 48.0 3.92e-01 91.3% 95.6%
3927652 2484.5.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase 0.56 36.0 4.22e-01 85.1% 93.6%
5064853 2002.1.1.101 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Orn_Arg_deC_N 0.56 38.0 3.06e-01 70.2% 36.4%
4964713 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.55 42.0 4.47e-01 87.6% 91.4%
3944443 2484.1.1.21 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › BcrAD_BadFG 0.54 47.0 3.97e-01 91.3% 99.6%
2390921 7579.1.1.9 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Esterase 0.53 45.0 3.70e-01 91.9% 48.8%
5048618 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.53 40.0 4.35e-01 85.7% 94.1%
3287439 7579.1.1.9 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Esterase 0.53 45.0 3.72e-01 91.9% 58.6%
None — 0.52 44.0 3.63e-01 90.7% 50.2%
4012011 7579.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.52 43.0 3.56e-01 89.4% 51.7%
4975222 2004.1.1.191 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.52 44.0 4.08e-01 90.1% 99.0%
4354585 2003.1.1.61 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › KR 0.52 43.0 3.60e-01 90.1% 80.7%
5014519 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.52 41.0 4.30e-01 84.5% 90.7%
3239250 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.51 47.0 3.55e-01 100.0% 95.3%
3270756 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.51 42.0 4.27e-01 94.4% 89.0%
5051874 2006.1.6.15 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › DUF58 0.51 43.0 3.92e-01 90.7% 89.9%
4986005 2484.1.1.333 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF1464 0.51 46.0 4.63e-01 96.9% 100.0%