SMTL ID : 7wbb.1

Cryo-EM structure of substrate engaged Drg1 hexamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: A.246, V.247, G.248, L.250, P.288, G.289, T.290, G.291, K.292, T.293, M.294, Q.346, A.455, T.458 Chain B: R.401 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain A Salt bridges: B:R.401, B:R.401, A:K.292 Hydrogen bonds: A:G.248, A:G.248, A:G.289, A:G.289, A:G.291, A:K.292, A:T.293, A:T.293, A:T.293, A:M.294, A:Q.346, A:T.458 ATP.2: 16 residues within 4Å: Chain A: D.517, I.518, G.519, G.560, C.561, S.562, K.563, T.564, L.565, Q.617, I.692, G.721, A.722 Chain B: D.645, R.671, R.674 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.519, A:G.519, A:G.560, A:C.561, A:S.562, A:S.562, A:K.563, A:T.564, A:T.564, A:L.565, A:Q.617, B:D.645 Salt bridges: A:K.563, A:K.563, B:R.671, B:R.671, B:R.671, B:R.674 ATP.3: 18 residues within 4Å: Chain B: V.247, G.248, G.289, T.290, G.291, K.292, T.293, M.294, R.297, N.390, I.422, Q.426, G.454, A.455, T.458 Chain G: D.375, R.401, R.404 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain G 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:M.294, B:R.297, B:Q.346, B:N.390, B:T.458, G:D.375 Salt bridges: B:K.292, B:K.292, G:R.401, G:R.404 ATP.4: 19 residues within 4Å: Chain B: D.517, I.518, G.519, G.520, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, Q.617, I.692, G.721, A.722 Chain G: D.645, R.671, R.674 19 PLIP interactions: 4 interactions with chain G, 15 interactions with chain B Salt bridges: G:R.671, G:R.671, G:R.671, G:R.674, B:K.563, B:K.563, B:K.568 Hydrogen bonds: B:G.519, B:G.520, B:G.560, B:C.561, B:S.562, B:S.562, B:K.563, B:T.564, B:T.564, B:L.565, B:K.568, B:Q.617 ATP.5: 18 residues within 4Å: Chain C: A.246, V.247, G.248, G.289, T.290, G.291, K.292, T.293, M.294, Q.346, N.390, I.422, G.454, A.455, T.458 Chain D: D.375, R.401, R.404 20 PLIP interactions: 15 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.248, 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:M.294, C:Q.346, C:N.390, C:T.458, D:D.375 Salt bridges: C:K.292, C:K.292, D:R.401, D:R.401, D:R.401, D:R.404 ATP.6: 18 residues within 4Å: Chain C: D.517, I.518, G.519, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, Q.617, N.660, I.692, A.722, V.725 Chain D: R.671, R.674 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.517, C:D.517, C:G.519, C:G.560, C:C.561, C:K.563, C:T.564, C:T.564, C:L.565, C:Q.617, C:N.660, C:N.660 Salt bridges: C:K.563, D:R.671, D:R.671, D:R.674 ATP.7: 12 residues within 4Å: Chain D: A.246, 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 D Hydrogen bonds: D:G.289, D:G.291, D:K.292, D:T.293, D:T.293, D:M.294, D:N.390, D:T.458 Salt bridges: D:K.292 ATP.8: 10 residues within 4Å: Chain D: G.519, G.560, S.562, K.563, T.564, L.565, N.660, I.692, A.722, V.725 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.519, D:C.561, D:S.562, D:S.562, D:S.562, D:K.563, D:T.564, D:T.564, D:T.564, D:L.565, D:N.660 Salt bridges: D:K.563 ATP.9: 15 residues within 4Å: Chain A: R.401 Chain E: V.247, G.248, L.250, P.288, G.289, T.290, G.291, K.292, T.293, M.294, N.390, I.422, G.454, T.458 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:G.248, E:G.289, E:G.291, E:K.292, E:T.293, E:M.294, E:N.390, E:N.390, E:T.458 Salt bridges: E:K.292, A:R.401, A:R.401, A:R.401 ATP.10: 18 residues within 4Å: Chain C: D.375, R.401, R.404 Chain G: A.246, V.247, G.248, P.288, G.289, T.290, G.291, K.292, T.293, M.294, I.422, Q.426, G.454, A.455, T.458 15 PLIP interactions: 4 interactions with chain C, 11 interactions with chain G Salt bridges: C:R.401, C:R.401, C:R.401, C:R.404, G:K.292, G:K.292 Hydrogen bonds: G:G.248, G:G.248, G:G.289, G:G.291, G:K.292, G:T.293, G:T.293, G:M.294, G:T.458 ATP.11: 17 residues within 4Å: Chain C: D.645, R.671, R.674 Chain G: D.517, G.519, P.559, G.560, C.561, S.562, K.563, T.564, L.565, Q.617, N.660, I.692, G.721, A.722 15 PLIP interactions: 11 interactions with chain G, 4 interactions with chain C Hydrogen bonds: G:G.519, G:G.519, G:G.560, G:C.561, G:S.562, G:K.563, G:T.564, G:T.564, G:L.565, G:Q.617 Salt bridges: G:K.563, C:R.671, C:R.671, C:R.671, C:R.674

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

2022-12-28

Peptides

AFG2 isoform 1: ABCDEG
substrate: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

G
C

F
H

AFG2 isoform 1

substrate

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