SMTL ID : 8dgc.1

Avs3 bound to phage PhiV-1 terminase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: I.259, N.261, S.262, V.263, D.288, A.289, G.290, V.291, G.292, K.293, S.294, I.295, R.429, P.482, R.483, A.486 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.262, A:V.263, A:G.290, A:V.291, A:G.292, A:K.293, A:S.294, A:S.294, A:I.295 Salt bridges: A:K.293, A:K.293, A:R.429, A:R.483, A:R.483, A:R.483 ATP.3: 14 residues within 4Å: Chain B: I.259, S.262, V.263, A.289, G.290, V.291, G.292, K.293, S.294, I.295, R.429, P.482, R.483 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:V.263, B:V.263, B:A.289, B:G.290, B:V.291, B:G.292, B:K.293, B:S.294, B:S.294, B:I.295 Salt bridges: B:K.293, B:K.293, B:R.429, B:R.483, B:R.483, B:R.483 ATP.5: 17 residues within 4Å: Chain C: I.259, N.261, S.262, V.263, D.288, A.289, G.290, V.291, G.292, K.293, S.294, I.295, R.429, P.482, R.483, A.486 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.262, C:V.263, C:G.290, C:V.291, C:G.292, C:K.293, C:S.294, C:S.294, C:I.295 Salt bridges: C:K.293, C:K.293, C:R.429, C:R.483, C:R.483, C:R.483 ATP.7: 14 residues within 4Å: Chain D: I.259, S.262, V.263, A.289, G.290, V.291, G.292, K.293, S.294, I.295, R.429, P.482, R.483 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:V.263, D:V.263, D:A.289, D:G.290, D:V.291, D:G.292, D:K.293, D:S.294, D:S.294, D:I.295 Salt bridges: D:K.293, D:K.293, D:R.429, D:R.483, D:R.483, D:R.483 ATP.9: 16 residues within 4Å: Chain A: Y.1714, H.1770 Chain E: W.28, L.33, P.34, K.35, Q.40, R.61, G.62, I.63, G.64, K.65, S.66, F.67, R.266 Ligands: MG.10 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Q.40, E:Q.40, E:G.62, E:I.63, E:G.64, E:K.65, E:S.66, E:S.66, E:R.266, A:Y.1714 Salt bridges: E:R.61, E:K.65, E:K.65 pi-Cation interactions: E:R.266, E:R.266 ATP.11: 15 residues within 4Å: Chain B: Y.1714, H.1770 Chain F: W.28, P.34, K.35, Q.40, R.61, G.62, I.63, G.64, K.65, S.66, F.67, R.266 Ligands: MG.12 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Q.40, F:Q.40, F:G.62, F:I.63, F:G.64, F:K.65, F:S.66, F:S.66, F:R.266, B:Y.1714 Salt bridges: F:R.61, F:K.65, F:K.65 pi-Cation interactions: F:R.266, F:R.266 ATP.13: 16 residues within 4Å: Chain C: Y.1714, H.1770 Chain G: W.28, L.33, P.34, K.35, Q.40, R.61, G.62, I.63, G.64, K.65, S.66, F.67, R.266 Ligands: MG.14 15 PLIP interactions: 14 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:Q.40, G:Q.40, G:G.62, G:I.63, G:G.64, G:K.65, G:S.66, G:S.66, G:R.266, C:Y.1714 Salt bridges: G:R.61, G:K.65, G:K.65 pi-Cation interactions: G:R.266, G:R.266 ATP.15: 15 residues within 4Å: Chain D: Y.1714, H.1770 Chain H: W.28, P.34, K.35, Q.40, R.61, G.62, I.63, G.64, K.65, S.66, F.67, R.266 Ligands: MG.16 16 PLIP interactions: 2 interactions with chain D, 14 interactions with chain H Hydrogen bonds: D:Y.1714, D:H.1770, H:Q.40, H:Q.40, H:G.62, H:I.63, H:G.64, H:K.65, H:S.66, H:S.66, H:R.266 Salt bridges: H:R.61, H:K.65, H:K.65 pi-Cation interactions: H:R.266, H:R.266

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.294 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.294 MG.4: 2 residues within 4Å: Chain B: S.294 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.294 MG.6: 2 residues within 4Å: Chain C: S.294 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.294 MG.8: 2 residues within 4Å: Chain D: S.294 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.294 MG.10: 3 residues within 4Å: Chain A: Y.1714 Chain E: S.66 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: Y.1714 Chain F: S.66 Ligands: ATP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: Y.1714 Chain G: S.66 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain D: Y.1714 Chain H: S.66 Ligands: ATP.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, L.A. et al., Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science (2022)

Release Date

2022-08-03

Peptides

SeAvs3: ABCD
Terminase, large subunit: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

SeAvs3

Terminase, large subunit