←Back to structures

MW349128.1__QQO92610.1__CPT_Machias_234__00216

Bact-Vir

MW349128.1__QQO92610.1__CPT_Machias_234__00216

Identity

Accession:
MW349128 ↗
Kingdom:
phage

Quality

87.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Staphylococcus_phage_Machias

TaxID: 2797423

Cluster

View cluster (34 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 13-78
PDB
Domain cluster: rep: MK448748.1__QBX17976.1__Javan389_0017__00017__D13-80
CATH (15)
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 › 0.85 64.0 5.42e-01 100.0% 50.0%
6toaE01 2.40.10.270 Mainly Beta › Beta Barrel › Thrombin, subunit H › Bacteriophage SPP1 head-tail adaptor protein 0.60 35.0 3.12e-01 84.8% 37.8%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.59 35.0 3.55e-01 97.0% 60.0%
2yh6D00 3.30.530.50 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.57 45.0 3.99e-01 93.9% 80.9%
3iiiA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 44.0 3.00e-01 90.9% 39.9%
7ob9B01 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 0.55 48.0 3.49e-01 100.0% 78.1%
1vq8Q00 2.30.30.70 Mainly Beta › Roll › SH3 type barrels. › Ribosomal protein L21 0.53 36.0 3.22e-01 100.0% 49.5%
1dfvA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 42.0 3.16e-01 89.4% 65.9%
6gfaA02 3.30.30.30 Alpha Beta › 2-Layer Sandwich › Defensin A-like › 0.52 37.0 3.93e-01 83.3% 89.3%
3oe3C00 2.40.128.200 Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor 0.52 42.0 3.90e-01 93.9% 95.5%
1v1qA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 40.0 3.47e-01 89.4% 82.7%
2gy5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 41.0 3.65e-01 90.9% 92.9%
2f96A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 36.0 2.65e-01 75.8% 99.5%
3d2fA02 3.30.30.30 Alpha Beta › 2-Layer Sandwich › Defensin A-like › 0.51 42.0 4.11e-01 95.5% 100.0%
8aa9A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 35.0 2.99e-01 72.7% 61.4%
ECOD (14)
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 0.70 62.0 5.10e-01 98.5% 55.7%
4211951 2.1.1.14 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RuvA_N 0.69 36.0 3.43e-01 93.9% 42.5%
3926624 4184.1.1.0 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat 0.68 39.0 4.36e-01 97.0% 74.0%
3644383 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.64 46.0 4.04e-01 75.8% 81.0%
3236774 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.58 38.0 2.44e-01 100.0% 13.5%
200073 10.12.1.39 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.58 41.0 3.16e-01 77.3% 46.6%
3236279 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.57 37.0 2.41e-01 100.0% 14.8%
3941391 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 33.0 3.46e-01 98.5% 61.7%
3719862 5.1.3.116 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_KLHDC2_KLHL20_DRC7 0.56 41.0 2.66e-01 81.8% 32.6%
1792552 4.1.1.19 ↗ beta barrels › SH3 › SH3 › SH3 › LSM 0.54 33.0 3.68e-01 87.9% 81.2%
4024671 4041.1.1.0 ↗ 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 0.51 40.0 3.02e-01 89.4% 90.0%
3507374 391.1.1.7 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2 0.51 36.0 3.39e-01 84.8% 61.3%
5069121 4.6.1.0 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain 0.51 37.0 3.84e-01 78.8% 100.0%
3512439 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.51 35.0 3.36e-01 84.8% 61.3%
D2 medium residues 79-144
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13392.13 best HNH_3 28.1 1.70e-06 48.5% 47.8%
CATH (2)
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 › 0.86 62.0 5.15e-01 77.3% 46.2%
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 53.0 4.10e-01 98.5% 46.9%
ECOD (6)
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 0.83 60.0 4.90e-01 77.3% 43.5%
4303143 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.79 59.0 5.39e-01 78.8% 63.5%
4949181 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.72 63.0 6.03e-01 97.0% 93.3%
5080086 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.66 51.0 4.85e-01 86.4% 82.5%
3839706 378.1.1.30 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › PF30178 0.65 57.0 4.79e-01 100.0% 86.1%
3924550 4026.1.1.0 ↗ a+b three layers › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) 0.53 36.0 2.89e-01 74.2% 87.7%