SMTL ID : 9cdb.1

CryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in cA6 (partial density) bound form with ATP (partial density).

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

A-A-A.1: 15 residues within 4Å: Chain A: G.10, H.11, S.12, G.102, N.130, R.132 Chain B: A.9, G.10, H.11, S.12, S.100, G.101, G.102, I.103, K.104 Protein-ligand interaction information (PLIP) not available A-A-A.2: 10 residues within 4Å: Chain E: G.10, H.11, S.12, G.102, A.127, N.130 Chain F: H.11, S.12, N.130, R.132 Protein-ligand interaction information (PLIP) not available A-A-A.3: 9 residues within 4Å: Chain C: H.11, S.12, N.130 Chain D: H.11, S.12, M.14, G.102, I.103, N.130 Protein-ligand interaction information (PLIP) not available

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

ATP.4: 6 residues within 4Å: Chain A: A.328, F.372, Y.373, E.581, L.582, F.585 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.373, A:Y.373, A:E.581 pi-Stacking: A:F.585, A:F.585 ATP.5: 7 residues within 4Å: Chain A: G.247, G.297, N.298, G.301, S.302, N.338, Y.339 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.294, A:M.294, A:N.298, A:S.302, A:N.338, A:Y.339 ATP.7: 7 residues within 4Å: Chain B: R.162, K.165, N.370, F.372, Y.373, F.585, R.588 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.162, B:Y.373, B:Y.373, B:R.588, B:R.588 Salt bridges: B:K.165, B:K.165, B:R.588 pi-Stacking: B:Y.373 ATP.8: 13 residues within 4Å: Chain B: G.247, G.248, M.294, G.297, N.298, N.300, G.301, S.302, N.338, Y.339, S.383, A.419, G.420 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.247, B:G.297, B:N.300, B:S.302, B:S.302, B:N.338, B:S.383, B:S.383, B:G.420 pi-Stacking: B:H.245 ATP.10: 3 residues within 4Å: Chain C: F.372, Y.373, F.585 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.373, C:Y.373 pi-Stacking: C:F.585, C:F.585 ATP.11: 7 residues within 4Å: Chain C: H.245, G.247, G.297, N.300, G.301, S.302, N.338 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.245, C:G.297, C:S.302, C:S.302, C:N.338 ATP.13: 5 residues within 4Å: Chain D: K.165, F.372, Y.373, F.585, R.588 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.373, D:Y.373, D:R.588, D:R.588 Salt bridges: D:K.165, D:R.588 ATP.14: 12 residues within 4Å: Chain D: G.247, G.248, M.294, G.297, N.298, N.300, G.301, S.302, N.338, S.383, A.419, G.420 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.297, D:N.300, D:S.302, D:S.383, D:S.383 Salt bridges: D:K.303 pi-Stacking: D:H.245, D:H.245 ATP.16: 6 residues within 4Å: Chain E: A.328, F.372, Y.373, E.581, L.582, F.585 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.373, E:Y.373, E:E.581 pi-Stacking: E:F.585, E:F.585 ATP.17: 10 residues within 4Å: Chain E: G.247, G.248, M.294, G.301, S.302, N.338, Y.339, A.419, H.448, N.534 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.247, E:N.338, E:Y.339, E:Y.339, E:H.448 ATP.19: 9 residues within 4Å: Chain F: D.91, R.162, K.165, N.370, F.372, Y.373, E.581, F.585, R.588 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.91, F:Y.373, F:R.588 Salt bridges: F:R.162, F:K.165, F:R.588 ATP.20: 15 residues within 4Å: Chain F: G.247, G.248, L.290, M.294, G.297, N.298, N.300, G.301, S.302, N.338, Y.339, I.381, S.383, A.419, G.420 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.297, F:G.297, F:S.302, F:N.338, F:Y.339, F:S.383, F:S.383, F:G.420 pi-Cation interactions: F:H.245

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: H.243, H.245, H.448, D.533 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.243, A:H.245, A:H.448, A:D.533 MG.9: 4 residues within 4Å: Chain B: H.243, H.245, H.448, D.533 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.243, B:H.245, B:H.448, B:D.533 MG.12: 4 residues within 4Å: Chain C: H.243, H.245, H.448, D.533 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.243, C:H.245, C:H.448, C:D.533 MG.15: 4 residues within 4Å: Chain D: H.243, H.245, H.448, D.533 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.243, D:H.245, D:H.448, D:D.533 MG.18: 4 residues within 4Å: Chain E: H.243, H.245, H.448, D.533 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.243, E:H.245, E:D.533 MG.21: 4 residues within 4Å: Chain F: H.243, H.245, H.448, D.533 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.243, F:H.245, F:H.448, F:D.533

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baca, C.F. et al., The CRISPR-associated adenosine deaminase Cad1 converts ATP to ITP to provide antiviral immunity. Cell (2024)

Release Date

2024-10-30

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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