SMTL ID : 9c77.1

cryoEM structure of CRISPR associated effector, CARF-Adenosine deaminase 1, Cad1, in cA4 bound form with ATP.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

A-A-A-A.1: 31 residues within 4Å: Chain A: A.9, G.10, H.11, S.12, M.14, V.15, E.18, T.35, D.67, G.102, I.103, M.106, L.126, A.127, N.130 Chain B: G.10, H.11, S.12, M.14, V.15, E.18, K.39, D.67, S.100, G.102, I.103, K.104, V.125, L.126, A.127, N.130 Protein-ligand interaction information (PLIP) not available A-A-A-A.2: 31 residues within 4Å: Chain C: G.10, H.11, S.12, M.14, V.15, E.18, T.35, D.67, G.102, I.103, K.104, M.106, V.125, L.126, A.127, N.130 Chain D: G.10, H.11, S.12, V.15, E.18, K.39, D.67, G.102, I.103, K.104, V.125, L.126, A.127, N.130, I.146 Protein-ligand interaction information (PLIP) not available A-A-A-A.3: 30 residues within 4Å: Chain E: A.9, G.10, H.11, M.14, K.39, D.67, G.102, I.103, K.104, M.106, L.126, A.127, D.128, N.130 Chain F: G.10, H.11, S.12, V.15, E.18, K.39, D.67, S.100, G.101, G.102, I.103, K.104, V.125, L.126, A.127, N.130 Protein-ligand interaction information (PLIP) not available

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

ATP.4: 6 residues within 4Å: Chain A: F.372, Y.373, C.374, E.581, L.582, F.585 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.328, A:Y.373 pi-Stacking: A:Y.373, A:F.585, A:F.585 ATP.5: 14 residues within 4Å: Chain A: H.245, L.246, G.247, G.248, L.290, M.294, G.301, S.302, S.335, N.338, Y.339, I.381, S.383 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.247, A:F.249, A:N.300, A:S.302, A:S.335, A:N.338, A:Y.339, A:S.383 pi-Stacking: A:H.448, A:H.448 ATP.7: 8 residues within 4Å: Chain B: Q.371, F.372, Y.373, F.578, E.581, L.582, F.585, R.588 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.373, B:E.581 Salt bridges: B:R.588, B:R.588 pi-Stacking: B:F.585, B:F.585 ATP.8: 14 residues within 4Å: Chain B: G.247, G.297, N.298, N.300, G.301, S.302, S.335, N.338, Y.339, I.381, S.383, A.419, G.420, F.421 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.297, B:N.300, B:S.302, B:S.335, B:N.338, B:N.338, B:Y.339, B:S.383, B:S.383 pi-Stacking: B:H.448 ATP.10: 5 residues within 4Å: Chain C: F.372, Y.373, E.581, L.582, F.585 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.373, C:Y.373, C:Y.373, C:E.581, C:E.581 pi-Stacking: C:F.585, C:F.585 ATP.11: 16 residues within 4Å: Chain C: H.245, G.247, G.248, L.290, M.294, G.297, N.298, N.300, G.301, S.302, S.335, N.338, I.381, A.419, G.420, H.448 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.247, C:S.302, C:S.335, C:N.338, C:N.338 ATP.13: 6 residues within 4Å: Chain D: F.372, Y.373, E.581, L.582, F.585, R.588 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.373, D:E.581, D:E.581 Salt bridges: D:R.588, D:R.588 pi-Stacking: D:F.585, D:F.585 ATP.14: 16 residues within 4Å: Chain D: H.245, G.247, M.294, G.297, N.298, N.300, G.301, S.302, S.335, N.338, Y.339, S.383, A.419, G.420, H.448 Ligands: MG.15 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.247, D:G.297, D:G.297, D:S.302, D:S.335, D:N.338, D:N.338, D:G.420 pi-Stacking: D:H.245 pi-Cation interactions: D:H.448 ATP.16: 6 residues within 4Å: Chain E: F.372, Y.373, F.578, 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: 15 residues within 4Å: Chain E: H.245, G.247, G.297, N.300, G.301, S.302, S.335, N.338, Y.339, S.383, F.386, A.419, G.420, F.421, H.448 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.297, E:N.300, E:S.302, E:S.335, E:S.335, E:N.338, E:Y.339, E:S.383, E:S.383, E:H.448 pi-Stacking: E:H.448 ATP.19: 6 residues within 4Å: Chain F: F.372, Y.373, E.581, L.582, F.585, R.588 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:Y.373, F:Y.373, F:E.581, F:E.581 Salt bridges: F:R.588, F:R.588 pi-Stacking: F:F.585, F:F.585 ATP.20: 16 residues within 4Å: Chain F: H.245, G.247, M.294, G.297, N.298, N.300, G.301, S.302, N.338, Y.339, I.381, S.383, A.419, G.420, H.448 Ligands: MG.21 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.297, F:G.297, F:S.302, F:N.338, F:S.383, F:G.420 pi-Stacking: F:H.448

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: H.243, H.245, H.448, D.533 Ligands: ATP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.243, A:H.245, 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 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.243, C:H.245, C:D.533 MG.15: 5 residues within 4Å: Chain D: H.243, H.245, H.448, D.533 Ligands: ATP.14 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: 5 residues within 4Å: Chain F: H.243, H.245, H.448, D.533 Ligands: ATP.20 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

Related Entries With Identical Sequence