←Back to structures

MN988556.1__QIG76678.1__EVC28_054__00054

Bact-Vir

MN988556.1__QIG76678.1__EVC28_054__00054

Identity

Accession:
MN988556 ↗
Kingdom:
phage

Quality

64.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_RHph_I1_23

TaxID: 2509727

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 53-106
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2f51A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.70 49.0 3.91e-01 74.1% 82.9%
2lstA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.70 48.0 3.72e-01 74.1% 72.3%
3q0xA01 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.70 49.0 3.49e-01 74.1% 79.4%
3ub1D02 3.10.450.540 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.68 48.0 3.74e-01 74.1% 87.7%
6oqrA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.65 54.0 4.69e-01 98.1% 74.4%
2gnxA02 3.30.450.240 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.62 43.0 3.52e-01 74.1% 41.3%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 46.0 3.66e-01 85.2% 71.1%
4azzA00 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.61 52.0 3.72e-01 98.1% 78.8%
2zkmX01 2.30.29.240 Mainly Beta › Roll › PH-domain like › 0.61 48.0 3.22e-01 87.0% 49.5%
1su0B00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.60 44.0 3.37e-01 81.5% 80.1%
4hz9B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 40.0 3.15e-01 72.2% 93.5%
1tpmA00 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.59 40.0 4.11e-01 74.1% 78.0%
3ifvC00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.59 46.0 2.98e-01 85.2% 19.6%
1w4tA02 2.40.128.150 Mainly Beta › Beta Barrel › Lipocalin › Cysteine proteinases 0.58 43.0 3.65e-01 83.3% 100.0%
3cpxA02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.58 48.0 4.69e-01 100.0% 100.0%
1fu1A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.58 40.0 3.22e-01 74.1% 88.1%
2vgnA02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.58 42.0 3.24e-01 79.6% 89.0%
3vpbE00 2.20.28.160 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.57 37.0 3.67e-01 70.4% 62.5%
4nsxA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.57 40.0 2.57e-01 77.8% 41.2%
3holA03 2.40.128.240 Mainly Beta › Beta Barrel › Lipocalin › 0.56 42.0 3.64e-01 83.3% 59.6%
3nrlA00 2.40.10.390 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.56 46.0 4.35e-01 98.1% 97.1%
1wquA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.56 47.0 3.82e-01 100.0% 76.3%
5cw7B00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.56 40.0 3.32e-01 74.1% 54.3%
3j7yd00 3.10.450.240 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 39.0 2.90e-01 77.8% 80.2%
1jofA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 45.0 2.80e-01 98.1% 28.2%
4b9wA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.54 42.0 4.19e-01 85.2% 87.5%
5i47B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 40.0 3.35e-01 81.5% 77.9%
5wceA02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.54 41.0 3.17e-01 88.9% 35.7%
2jo6A00 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.54 41.0 3.40e-01 88.9% 91.8%
1uc8A03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 40.0 3.43e-01 83.3% 79.8%
1vpkA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.54 38.0 3.05e-01 88.9% 35.0%
2diqA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.54 46.0 3.83e-01 100.0% 56.0%
4h5iB00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 47.0 2.86e-01 100.0% 28.1%
2af5A01 2.40.128.160 Mainly Beta › Beta Barrel › Lipocalin › C1 set domains (antibody constant domain-like) 0.53 37.0 3.71e-01 75.9% 98.1%
2g8sB00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.53 43.0 2.73e-01 100.0% 89.0%
3zyyX03 3.10.20.880 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 44.0 3.76e-01 92.6% 96.6%
6ptrB01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.53 37.0 3.00e-01 88.9% 36.3%
5i4dA02 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 35.0 3.27e-01 70.4% 80.3%
5yxkA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 40.0 3.41e-01 98.1% 73.6%
1p9rA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.51 39.0 3.16e-01 85.2% 72.1%
6u5vB07 3.30.1120.100 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.51 37.0 2.91e-01 77.8% 68.2%
5yv7A00 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.50 36.0 3.53e-01 100.0% 70.0%
4exrA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.50 34.0 3.22e-01 72.2% 56.3%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4928895 79.1.1.0 ↗ beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain 0.74 51.0 3.27e-01 74.1% 16.4%
None — 0.69 47.0 3.15e-01 72.2% 21.1%
3308710 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.68 46.0 4.20e-01 85.2% 54.3%
4994059 2492.1.1.2 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB 0.68 46.0 3.52e-01 72.2% 60.7%
3405548 10.32.1.21 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › PAW 0.67 51.0 3.56e-01 83.3% 90.0%
4060488 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.65 54.0 4.90e-01 100.0% 92.5%
4039334 1001.1.1.1 ↗ a+b two layers › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Molybdop_Fe4S4 0.64 46.0 4.49e-01 77.8% 91.7%
4083044 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.64 53.0 4.87e-01 98.1% 98.7%
4066146 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.64 53.0 4.44e-01 100.0% 71.4%
4883586 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.64 53.0 4.72e-01 100.0% 87.2%
3298233 2007.1.2.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.64 45.0 3.27e-01 74.1% 31.6%
3642150 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.64 52.0 4.44e-01 96.3% 73.7%
4245518 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.63 52.0 4.78e-01 98.1% 96.0%
3811997 5.3.1.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II › S_locus_glycop 0.63 46.0 3.28e-01 77.8% 86.5%
3623169 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.63 45.0 3.76e-01 79.6% 57.1%
3451758 243.5.1.1 ↗ a+b two layers › Cystatin-like › Amine oxidase N-terminal region › Amine oxidase N-terminal region › Cu_amine_oxidN2 0.62 44.0 3.56e-01 74.1% 86.7%
5026400 1001.1.1.1 ↗ a+b two layers › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Molybdop_Fe4S4 0.62 44.0 4.23e-01 75.9% 76.9%
4937366 4312.1.1.3 ↗ a+b two layers › RelE-like › RelE-like › RelE-like › ParE_toxin 0.62 41.0 3.49e-01 70.4% 47.4%
4939349 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.62 42.0 3.43e-01 74.1% 72.2%
4618103 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.61 51.0 4.96e-01 96.3% 91.7%
3802041 2007.1.2.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.61 45.0 3.07e-01 79.6% 31.0%
4338601 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.61 50.0 4.42e-01 100.0% 78.9%
3164898 4.11.1.1 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S24 0.61 51.0 4.38e-01 100.0% 60.0%
3715939 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.60 50.0 3.52e-01 100.0% 42.9%
3602123 1.1.8.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › eIF2_C 0.60 48.0 4.37e-01 94.4% 74.4%
3939997 1.1.8.5 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › tRNA_Me_trans_C 0.60 49.0 4.23e-01 96.3% 64.4%
3214168 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 45.0 3.55e-01 85.2% 64.8%
3768845 4294.1.1.0 ↗ few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like 0.58 45.0 3.74e-01 88.9% 93.3%
2724185 4091.1.1.1 ↗ beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.57 49.0 3.54e-01 96.3% 90.4%
2488620 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 46.0 4.52e-01 94.4% 100.0%
4992358 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.57 43.0 3.26e-01 83.3% 33.3%
3177212 220.1.1.188 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_BUD3_C 0.57 43.0 3.22e-01 85.2% 72.7%
4463778 227.1.1.7 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_2 0.56 39.0 3.12e-01 88.9% 34.2%
4232371 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.56 43.0 3.37e-01 85.2% 39.2%
3881119 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.56 48.0 4.27e-01 100.0% 66.3%
3940997 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.56 47.0 3.57e-01 98.1% 58.5%
3509348 214.1.1.15 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7063, DUF7145 0.55 47.0 2.97e-01 100.0% 31.3%
3208203 375.1.1.19 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RNA_POL_M_15KD 0.55 34.0 3.42e-01 83.3% 60.0%
4646871 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.55 41.0 3.21e-01 83.3% 37.6%
3705938 5.1.2.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.54 42.0 3.39e-01 100.0% 41.7%
4591776 227.1.1.7 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_2 0.53 39.0 3.00e-01 88.9% 33.8%
3382115 226.1.1.20 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › PF30468, PF30469 0.53 39.0 2.73e-01 81.5% 28.6%
4969245 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.53 46.0 3.35e-01 100.0% 56.8%
3910825 5.1.3.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1 0.52 45.0 2.84e-01 100.0% 44.4%
3656401 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 45.0 4.11e-01 100.0% 81.3%
3809440 226.1.1.20 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › PF30468, PF30469 0.52 40.0 3.12e-01 85.2% 44.0%
3994860 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 44.0 2.72e-01 100.0% 26.5%
4941490 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.51 38.0 2.92e-01 83.3% 33.3%
4002078 384.1.1.1 ↗ few secondary structure elements › BPTI-like › BPTI-like › BPTI-like › Kunitz_BPTI 0.51 35.0 3.43e-01 100.0% 65.0%
4342778 5.1.3.4 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › WD40 0.51 43.0 2.48e-01 100.0% 13.8%
3744032 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.51 40.0 3.17e-01 100.0% 71.0%
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 0.51 38.0 3.13e-01 85.2% 79.1%
4024830 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.50 41.0 2.71e-01 98.1% 41.9%
3406312 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.50 37.0 2.99e-01 85.2% 39.8%
3245194 5.1.3.152 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Str_synth, SSL_N 0.50 44.0 2.66e-01 100.0% 15.6%