SMTL ID : 8z3r.1

The structure of type III CRISPR-associated deaminase in complex cA4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.264, H.266, H.471, D.569 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.264, A:H.266, A:H.471, A:D.569 ZN.3: 4 residues within 4Å: Chain B: H.264, H.266, H.471, D.569 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.264, B:H.266, B:H.471 ZN.5: 4 residues within 4Å: Chain C: H.264, H.266, H.471, D.569 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.264, C:H.266, C:H.471 ZN.7: 4 residues within 4Å: Chain D: H.264, H.266, H.471, D.569 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.264, D:H.266, D:H.471 ZN.9: 4 residues within 4Å: Chain E: H.264, H.266, H.471, D.569 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.264, E:H.266, E:H.471 ZN.10: 4 residues within 4Å: Chain F: H.264, H.266, H.471, D.569 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.264, F:H.266, F:H.471

6 x LQJ: 3'-O-[(R)-{[(2S,3aS,4S,6S,6aS)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]adenosine(Non-covalent)(Covalent)

LQJ.2: 19 residues within 4Å: Chain A: G.12, T.13, A.14, T.37, Q.67, G.102, G.103, F.104, K.105 Chain B: I.17, E.20, T.101, K.105, V.126, L.127, A.128, M.140, P.141 Ligands: LQJ.4 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.13, A:A.14, A:T.37, A:G.103, A:F.104, A:K.105, A:K.105, B:P.141 pi-Stacking: A:F.104, A:F.104 Salt bridges: B:K.105 LQJ.4: 19 residues within 4Å: Chain A: I.17, E.20, T.101, H.125, V.126, L.127, A.128, M.140, P.141 Chain B: G.12, T.13, A.14, T.37, Q.67, G.102, G.103, F.104, K.105 Ligands: LQJ.2 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:P.141, B:T.13, B:A.14, B:T.37, B:T.37, B:G.103, B:K.105, B:K.105 Salt bridges: A:K.105, A:H.125 pi-Stacking: B:F.104, B:F.104 LQJ.6: 20 residues within 4Å: Chain C: G.12, T.13, A.14, T.37, R.39, Q.67, G.102, G.103, F.104, K.105 Chain D: I.17, E.20, T.101, H.125, V.126, L.127, A.128, M.140, P.141 Ligands: LQJ.8 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.13, C:A.14, C:T.37, C:T.37, C:G.103, C:F.104, C:K.105, C:K.105, D:P.141 pi-Stacking: C:F.104 Salt bridges: D:H.125 LQJ.8: 19 residues within 4Å: Chain C: E.20, T.101, K.105, H.125, V.126, L.127, A.128, M.140, P.141 Chain D: G.12, T.13, A.14, T.37, Q.67, G.102, G.103, F.104, K.105 Ligands: LQJ.6 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.13, D:A.14, D:T.37, D:G.103, D:K.105, D:K.105, C:P.141 pi-Stacking: D:F.104, D:F.104 Salt bridges: C:K.105, C:H.125 LQJ.11: 20 residues within 4Å: Chain E: I.17, E.20, T.101, K.105, H.125, V.126, L.127, A.128, M.140, P.141 Chain F: G.12, T.13, A.14, T.37, Q.67, G.102, G.103, F.104, K.105 Ligands: LQJ.12 12 PLIP interactions: 3 interactions with chain E, 9 interactions with chain F Hydrogen bonds: E:P.141, F:T.13, F:T.37, F:T.37, F:G.103, F:K.105, F:K.105 Salt bridges: E:K.105, E:H.125, F:K.105 pi-Stacking: F:F.104, F:F.104 LQJ.12: 20 residues within 4Å: Chain E: G.12, T.13, A.14, T.37, R.39, Q.67, G.102, G.103, F.104, K.105 Chain F: I.17, E.20, T.101, K.105, V.126, L.127, A.128, M.140, P.141 Ligands: LQJ.11 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:T.13, E:T.37, E:G.103, E:K.105, F:P.141 pi-Stacking: E:F.104 Salt bridges: F:K.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Antiviral signaling of a type III CRISPR-associated deaminase. Science (2025)

Release Date

2024-12-25

Peptides

Adenosine deaminase domain-containing protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Adenosine deaminase domain-containing protein

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