SMTL ID : 8z3k.1

The structure of type III CRISPR-associated deaminase in complex 2cA6-2ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

2 x A- A- A- A- A- A: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')(Non-covalent)

A-A-A-A-A-A.1: 41 residues within 4Å: Chain A: G.12, T.13, A.14, A.16, I.17, E.20, T.37, Q.67, D.68, T.101, G.102, G.103, F.104, K.105, H.125, V.126, L.127, A.128, D.129, M.140, P.141 Chain B: G.12, T.13, A.14, I.17, E.20, T.37, Q.67, D.68, T.101, G.102, G.103, F.104, K.105, H.125, V.126, L.127, A.128, D.129, M.140, P.141 Protein-ligand interaction information (PLIP) not available A-A-A-A-A-A.2: 41 residues within 4Å: Chain C: G.12, T.13, A.14, I.17, T.37, R.39, D.68, T.101, G.102, G.103, F.104, K.105, H.125, V.126, L.127, A.128, D.129, D.130, M.140, P.141 Chain D: G.12, T.13, A.14, I.17, E.20, T.37, Q.67, D.68, K.70, T.101, G.102, G.103, F.104, K.105, H.125, V.126, L.127, A.128, D.129, M.140, P.141 Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain B: H.264, H.266, R.354, H.471, D.569 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.264, B:H.264, B:H.266, B:H.471 ZN.5: 6 residues within 4Å: Chain C: H.264, H.266, H.471, H.495, D.569 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.264, C:H.266, C:D.569

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

ATP.4: 20 residues within 4Å: Chain B: H.266, G.268, G.269, Y.314, M.315, G.322, T.323, S.356, N.359, Y.360, I.401, T.403, R.405, A.442, G.443, H.471, E.474, H.495, D.569, N.570 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.268, B:T.323, B:T.323, B:S.356, B:N.359, B:G.443, B:D.569, B:N.570 Salt bridges: B:R.405 pi-Stacking: B:H.266 pi-Cation interactions: B:H.471 ATP.6: 20 residues within 4Å: Chain C: H.266, G.268, M.315, G.318, N.321, G.322, T.323, S.356, Y.360, I.401, T.403, R.405, A.442, G.443, H.471, E.474, H.495, D.569, N.570 Ligands: ZN.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.268, C:G.269, C:G.318, C:T.323, C:Y.360, C:R.405, C:G.443, C:H.471, C:H.495 pi-Cation interactions: C:H.471

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

2024-12-11

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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