SMTL ID : 7ykk.1

Cryo-EM structure of Drg1 hexamer treated with ADP

Coordinates

PDB Format Compare

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, K.292, T.293, M.294, I.422, K.425, G.454, A.455, T.458 Chain B: R.401 12 PLIP interactions: 2 interactions with chain B, 10 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:T.293, A:M.294, A:K.425, A:T.458 Salt bridges: B:R.401, A:K.292 ATP.2: 15 residues within 4Å: Chain B: A.246, V.247, G.248, P.287, P.288, G.289, T.290, G.291, K.292, T.293, M.294, K.425, G.454, A.455, T.458 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.246, B:G.248, B:G.289, B:T.290, B:T.290, B:G.291, B:K.292, B:T.293, B:M.294, B:T.458 Salt bridges: B:K.292, B:K.292 ATP.3: 12 residues within 4Å: Chain C: P.288, G.289, T.290, G.291, K.292, T.293, M.294, R.297, I.422, G.454, A.455, T.458 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.289, C:T.290, C:G.291, C:T.293, C:T.293, C:T.293, C:M.294, C:R.297, C:N.390, C:T.458 Salt bridges: C:K.292 ATP.4: 11 residues within 4Å: Chain D: G.289, T.290, G.291, K.292, T.293, M.294, R.297, D.345, I.422, G.454, A.455 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.289, D:T.290, D:T.290, D:G.291, D:K.292, D:T.293, D:T.293, D:T.293, D:M.294, D:R.297, D:D.345 Salt bridges: D:K.292, D:K.292 ATP.5: 13 residues within 4Å: Chain E: P.288, G.289, T.290, G.291, K.292, T.293, M.294, N.390, I.422, G.454, A.455, T.458 Chain F: R.404 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.289, E:T.290, E:T.290, E:G.291, E:K.292, E:T.293, E:M.294, E:T.458 Salt bridges: E:K.292, E:K.292 ATP.6: 15 residues within 4Å: Chain F: A.246, V.247, G.248, L.250, G.289, T.290, G.291, K.292, T.293, M.294, D.345, I.422, G.454, A.455, T.458 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.248, F:G.248, F:G.289, F:T.290, F:T.290, F:G.291, F:K.292, F:T.293, F:T.293, F:D.345, F:T.458, F:T.458

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
D

B
E

C
F

D
A

E
B

F
C

ATPase family gene 2 protein

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