←Back to structures

MK620899.1__QBZ72770.1__SEA_GODONK_182__00151

Bact-Vir

MK620899.1__QBZ72770.1__SEA_GODONK_182__00151

Identity

Accession:
MK620899 ↗
Kingdom:
phage

Quality

83.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Godonkavirus› Gordonia_phage_GodonK

TaxID: 2562192

Cluster

View cluster (6 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 medium residues 2-77
PDB
Domain cluster: rep: S2_012_000_R2_scaffold_0_prodigal-single.1__X__X__00803__D8-94
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.87 80.0 7.47e-01 100.0% 90.2%
1yd0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.78 66.0 6.28e-01 100.0% 79.8%
3oqgA00 3.40.1440.50 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.76 57.0 4.32e-01 80.3% 48.3%
5fmvA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.68 40.0 3.94e-01 77.6% 52.4%
2a74A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.62 40.0 3.62e-01 76.3% 47.6%
3cu7A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.60 39.0 3.52e-01 76.3% 47.2%
2xbzA00 2.60.40.2380 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 37.0 3.09e-01 77.6% 37.1%
4blqA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 44.0 3.09e-01 86.8% 71.2%
6s2wA01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.56 40.0 3.93e-01 75.0% 72.0%
2bv4A00 2.60.120.400 Mainly Beta › Sandwich › Jelly Rolls › Calcium-mediated lectin 0.56 34.0 3.04e-01 76.3% 41.6%
2qsdB02 3.50.100.10 Alpha Beta › 3-Layer(bba) Sandwich › protein il1583 fold › protein il1583 domain 0.55 42.0 4.20e-01 98.7% 79.5%
2jmuA01 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.55 46.0 3.48e-01 100.0% 80.8%
4oumA00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.55 36.0 3.03e-01 76.3% 39.4%
4dqnA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.54 43.0 3.40e-01 85.5% 84.2%
1ajwA00 2.70.50.30 Mainly Beta › Distorted Sandwich › Coagulation Factor XIII; Chain A, domain 1 › Coagulation Factor XIII, subunit A, domain 1 0.54 39.0 3.18e-01 77.6% 40.7%
4fkeA03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 33.0 3.22e-01 75.0% 54.0%
1mgtA01 3.30.160.70 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Methylated DNA-protein cysteine methyltransferase domain 0.54 43.0 4.19e-01 100.0% 79.5%
6j7xC01 3.30.450.50 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin domain 0.53 40.0 3.36e-01 82.9% 86.4%
4f3jA00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.52 38.0 3.12e-01 77.6% 62.9%
2fgzA01 2.60.40.1130 Mainly Beta › Sandwich › Immunoglobulin-like › Rab geranylgeranyltransferase alpha-subunit, insert domain 0.52 37.0 3.24e-01 75.0% 66.1%
5eoxB03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 36.0 3.14e-01 75.0% 74.2%
6ryvA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 32.0 3.47e-01 72.4% 72.3%
2a90A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.52 38.0 3.57e-01 81.6% 82.7%
2pw9C03 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.51 35.0 3.00e-01 73.7% 50.0%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.51 38.0 3.70e-01 81.6% 100.0%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4947741 821.1.1.17 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF27096 0.82 72.0 6.95e-01 100.0% 84.7%
4929079 821.1.1.15 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › DUF7508 0.82 63.0 5.84e-01 100.0% 66.0%
4236834 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.82 72.0 6.91e-01 100.0% 84.7%
4945828 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.81 73.0 6.92e-01 100.0% 83.3%
4310838 821.1.1.9 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF30054 0.81 71.0 6.86e-01 100.0% 85.9%
4468826 821.1.1.9 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF30054 0.81 71.0 6.58e-01 100.0% 76.8%
4974405 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.81 72.0 6.80e-01 100.0% 82.2%
4515517 821.1.1.9 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF30054 0.80 71.0 6.74e-01 100.0% 82.2%
4977317 821.1.1.9 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF30054 0.80 71.0 6.07e-01 100.0% 62.2%
3588392 821.1.1.9 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF30054 0.78 70.0 6.39e-01 100.0% 75.0%
3965455 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.78 68.0 6.45e-01 100.0% 80.0%
5076894 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.78 70.0 5.37e-01 100.0% 53.5%
4170310 821.1.1.9 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF30054 0.77 68.0 6.47e-01 100.0% 83.3%
4346148 821.1.1.12 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF29812 0.75 67.0 5.69e-01 100.0% 65.6%
403748 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.74 57.0 4.35e-01 81.6% 50.0%
3363261 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.71 63.0 5.23e-01 100.0% 58.5%
4966592 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.67 36.0 4.06e-01 73.7% 69.1%
3414473 323.1.1.6 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Carn_acyltransf 0.63 47.0 2.81e-01 80.3% 45.5%
4595878 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.60 41.0 3.89e-01 75.0% 57.9%
3397211 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.58 50.0 3.91e-01 98.7% 52.4%
5068280 244.4.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › Ni-Fe binding domain in nickel-iron hydrogenase large subunit 0.57 32.0 3.23e-01 100.0% 53.3%
4936587 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 42.0 2.91e-01 81.6% 98.2%
5015864 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.56 37.0 3.63e-01 72.4% 61.2%
5071420 268.1.1.0 ↗ a+b two layers › Sterol carrier protein-like › Sterol carrier protein, SCP-related › Sterol carrier protein, SCP-related 0.55 38.0 3.38e-01 72.4% 92.2%
3698238 11.1.1.644 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_Pom152 0.55 42.0 3.45e-01 81.6% 60.0%
4674401 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.55 32.0 2.88e-01 75.0% 40.0%
4026461 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.53 40.0 3.44e-01 81.6% 54.0%
3966577 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 37.0 2.94e-01 75.0% 55.9%
4057352 1119.1.1.1 ↗ a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.52 44.0 3.16e-01 97.4% 95.3%
3237567 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.52 34.0 3.87e-01 88.2% 92.7%
5035856 2484.2.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Methylated DNA-protein cysteine methyltransferase domain › Methylated DNA-protein cysteine methyltransferase domain 0.52 41.0 4.20e-01 100.0% 92.0%
1031012 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.51 35.0 2.95e-01 73.7% 46.9%
3493644 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.51 36.0 2.87e-01 76.3% 47.9%