SMTL ID : 7ykz.1

Cryo-EM structure of Drg1 hexamer in the planar state treated with ADP/AMPPNP/Diazaborine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 9 residues within 4Å: Chain A: P.559, G.560, C.561, K.563, T.564, L.565, N.660, V.725 Chain D: R.671 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A Salt bridges: D:R.671, A:K.563, A:K.563 Hydrogen bonds: A:T.564, A:N.660 ADP.5: 11 residues within 4Å: Chain B: D.517, I.518, G.519, G.560, C.561, K.563, T.564, L.565, D.616, I.692, K.695 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.517, B:D.517, B:G.519, B:K.563, B:T.564, B:T.564, B:L.565 ADP.8: 8 residues within 4Å: Chain C: G.560, C.561, K.563, T.564, L.565, E.617, I.692, V.725 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.560, C:T.564, C:E.617 Salt bridges: C:K.563, C:K.563 ADP.11: 10 residues within 4Å: Chain D: P.558, P.559, G.560, C.561, S.562, K.563, T.564, K.568, N.660, K.695 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:P.558, D:P.559, D:K.563, D:T.564, D:T.564, D:T.564, D:N.660, D:K.695 ADP.14: 10 residues within 4Å: Chain E: D.517, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, K.695 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:D.517, E:P.558, E:G.560, E:G.560, E:K.563, E:T.564 Salt bridges: E:K.563 ADP.17: 11 residues within 4Å: Chain F: D.517, P.559, G.560, C.561, S.562, K.563, T.564, L.565, K.568, C.696, V.725 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:P.559, F:S.562, F:K.563, F:T.564, F:T.564, F:K.568, F:K.568

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

ATP.2: 17 residues within 4Å: Chain A: A.246, V.247, G.248, P.287, P.288, G.289, T.290, G.291, K.292, T.293, M.294, E.346, I.422, G.454, A.455, T.458 Ligands: NDT.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.248, A:G.248, A:G.289, A:T.290, A:G.291, A:K.292, A:T.293, A:T.293, A:T.293, A:M.294, A:T.458 Salt bridges: A:K.292 ATP.6: 17 residues within 4Å: Chain B: V.247, G.248, L.250, P.288, G.289, T.290, G.291, K.292, T.293, M.294, D.345, I.422, R.429, G.454, A.455, T.458 Ligands: NDT.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.248, B:G.248, B:G.289, B:T.290, B:G.291, B:K.292, B:T.293, B:T.293, B:D.345, B:D.345, B:T.458 ATP.9: 14 residues within 4Å: Chain C: A.246, V.247, G.289, T.290, G.291, K.292, T.293, M.294, I.422, G.454, A.455, T.458 Chain F: R.401 Ligands: NDT.10 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.248, C:G.289, C:G.291, C:K.292, C:T.293, C:T.293, C:M.294, C:T.458, F:R.401 Salt bridges: C:K.292 ATP.12: 16 residues within 4Å: Chain B: R.401 Chain D: A.246, V.247, G.248, L.250, G.289, T.290, G.291, K.292, T.293, M.294, I.422, G.454, A.455, T.458 Ligands: NDT.13 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.248, D:G.248, D:G.289, D:T.290, D:G.291, D:K.292, D:T.293, D:M.294, D:T.458 Salt bridges: D:K.292, B:R.401 ATP.15: 15 residues within 4Å: Chain E: P.288, G.289, T.290, G.291, K.292, T.293, M.294, D.345, E.346, I.422, Q.426, G.454, A.455, T.458 Ligands: NDT.16 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.289, E:T.290, E:G.291, E:K.292, E:D.345, E:T.458 Salt bridges: E:K.292, E:K.292 ATP.18: 15 residues within 4Å: Chain F: A.246, V.247, G.248, P.288, G.289, T.290, G.291, K.292, T.293, M.294, I.422, G.454, A.455, T.458 Ligands: NDT.4 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.248, F:G.248, F:G.289, F:T.290, F:G.291, F:K.292, F:T.293, F:M.294, F:T.458 Salt bridges: F:K.292

6 x NDT: 2-(TOLUENE-4-SULFONYL)-2H-BENZO[D][1,2,3]DIAZABORININ-1-OL(Non-covalent)

NDT.3: 5 residues within 4Å: Chain A: M.294, R.429 Chain D: G.275, G.403 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.429 pi-Cation interactions: A:R.429 NDT.4: 9 residues within 4Å: Chain A: F.274, G.275, V.276, G.403 Chain F: M.294, R.429, T.458, R.462 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.429 pi-Cation interactions: F:R.429 NDT.7: 7 residues within 4Å: Chain B: M.294, Q.426, R.429 Chain E: G.275, V.276, G.403 Ligands: ATP.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:R.429, E:V.276 Hydrogen bonds: B:R.429 pi-Cation interactions: B:R.429 NDT.10: 9 residues within 4Å: Chain C: R.429, T.458, R.462 Chain F: G.275, V.276, S.277, P.402, G.403 Ligands: ATP.9 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:V.276, C:T.458 Hydrogen bonds: F:S.277 pi-Cation interactions: C:R.429 NDT.13: 7 residues within 4Å: Chain B: G.403 Chain D: M.294, Q.426, R.429, T.458, R.462 Ligands: ATP.12 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Q.426, D:R.429, D:T.458 NDT.16: 7 residues within 4Å: Chain C: S.277, G.403 Chain E: Q.426, R.429, T.458, R.462 Ligands: ATP.15 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:Q.426, E:R.429, E:R.429, E:T.458 pi-Cation interactions: E:R.429, E:R.462 Hydrogen bonds: C:S.277

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
F

C
B

D
E

E
A

F
C

ATPase family gene 2 protein

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