SMTL ID : 7ykt.1

Cryo-EM structure of Drg1 hexamer in helical state treated with ADP/AMPPNP/benzo-diazaborine

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 11 residues within 4Å: Chain A: G.289, T.290, G.291, K.292, T.293, M.294, I.422, G.454, A.455, T.458 Chain B: R.401 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:R.401, A:G.289, A:T.290, A:K.292, A:T.293, A:T.293, A:M.294, A:T.458 Salt bridges: A:K.292, A:K.292 ATP.3: 13 residues within 4Å: Chain B: L.250, P.288, G.289, T.290, G.291, K.292, T.293, M.294, I.422, Q.426, G.454, A.455, T.458 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:P.287, B:G.289, B:T.290, B:T.290, B:T.290, B:G.291, B:K.292, B:T.293, B:T.293, B:T.293, B:M.294, B:Q.426, B:T.458 Salt bridges: B:K.292 ATP.4: 11 residues within 4Å: Chain C: G.289, T.290, G.291, K.292, T.293, M.294, I.422, G.454, A.455, T.458 Chain D: R.404 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.289, C:G.291, C:K.292, C:T.293, C:T.293, C:M.294, C:T.458 Salt bridges: D:R.404 ATP.6: 14 residues within 4Å: Chain D: A.246, G.248, P.287, G.289, T.290, G.291, K.292, T.293, M.294, R.297, I.422, G.454, A.455, T.458 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.248, D:G.248, D:P.287, D:G.289, D:T.290, D:T.290, D:G.291, D:K.292, D:T.293, D:T.293, D:M.294, D:T.458 Salt bridges: D:K.292, D:R.297 ATP.8: 14 residues within 4Å: Chain E: V.247, G.248, L.250, P.287, P.288, G.289, T.290, G.291, K.292, T.293, M.294, G.454, A.455 Chain F: R.401 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.248, E:G.248, E:G.289, E:T.290, E:T.290, E:G.291, E:K.292, E:T.293, E:M.294, F:R.401 Salt bridges: E:K.292, E:K.292, F:R.401 ATP.9: 14 residues within 4Å: Chain A: R.401 Chain F: P.288, G.289, T.290, G.291, K.292, T.293, M.294, N.390, I.422, Q.426, G.454, A.455, T.458 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.289, F:T.290, F:G.291, F:K.292, F:T.293, F:T.293, F:T.293, F:M.294, F:N.390, F:T.458 Salt bridges: F:K.292, F:K.292, A:R.401

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 12 residues within 4Å: Chain A: G.560, K.563, T.564, L.565, K.568, D.616, E.617, I.692, K.695, G.721, A.722, V.725 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.560, A:T.564, A:K.568, A:K.568, A:K.695 Salt bridges: A:K.563 ADP.5: 14 residues within 4Å: Chain C: G.557, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, K.568, E.617, N.660, I.692, V.725 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.560, C:C.561, C:K.563, C:T.564, C:T.564, C:T.564, C:K.568, C:K.568, C:N.660, C:N.660 Salt bridges: C:K.563 ADP.7: 9 residues within 4Å: Chain D: D.517, G.560, C.561, S.562, K.563, T.564, L.565, K.568, E.617 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.517, D:G.560, D:K.563, D:T.564, D:L.565, D:K.568, D:K.568, D:E.617 Salt bridges: D:K.563

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, C. et al., Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition. Nat Commun (2022)

Release Date

2022-12-14

Peptides

ATPase family gene 2 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
A

C
B

D
C

E
D

F
E

ATPase family gene 2 protein

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