SMTL ID : 7ykl.1

Cryo-EM structure of Drg1 hexamer treated with AMPPNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 12 residues within 4Å: Chain A: P.288, G.289, T.290, G.291, K.292, T.293, M.294, N.390, I.422, G.454, A.455, T.458 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.289, A:T.290, A:G.291, A:K.292, A:T.293, A:T.293, A:T.458 Salt bridges: A:K.292, A:K.292 ATP.2: 11 residues within 4Å: Chain B: P.288, G.289, T.290, G.291, K.292, T.293, M.294, G.454, A.455, T.458 Chain C: R.401 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.289, B:T.290, B:G.291, B:K.292, B:T.293, B:T.293, B:T.293, B:M.294, B:N.390 Salt bridges: B:K.292, B:K.292, C:R.401 ATP.3: 12 residues within 4Å: Chain C: P.288, G.289, T.290, G.291, K.292, T.293, M.294, G.454, A.455, T.458 Chain D: D.375, R.401 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.289, C:T.290, C:T.290, C:T.290, C:G.291, C:K.292, C:T.293, C:T.293, C:T.458, D:D.375 ATP.4: 10 residues within 4Å: Chain D: G.289, T.290, G.291, K.292, T.293, M.294, I.422, G.454, A.455, T.458 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.289, D:G.291, D:K.292, D:T.293, D:T.293, D:T.293, D:M.294, D:T.458 ATP.5: 9 residues within 4Å: Chain E: G.289, T.290, G.291, K.292, T.293, M.294, G.454, A.455, T.458 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.289, E:G.291, E:K.292, E:T.293, E:T.293, E:T.293, E:T.458 Salt bridges: E:K.292, E:K.292 ATP.6: 13 residues within 4Å: Chain A: R.404 Chain F: P.288, G.289, T.290, G.291, K.292, T.293, M.294, E.346, I.422, G.454, A.455, T.458 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.289, F:G.291, F:K.292, F:T.293, F:T.293, F:M.294, F:E.346, F:T.458 Salt bridges: A:R.404

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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