SMTL ID : 7z11.1

Structure of substrate bound DRG1 (AFG2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

11 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 15 residues within 4Å: Chain A: A.246, G.248, G.289, T.290, G.291, K.292, T.293, M.294, E.346, I.422, G.454, A.455, T.458 Chain B: R.401, R.404 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B 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, B:R.404, B:R.404 Salt bridges: A:K.292, B:R.401, B:R.401 AGS.2: 17 residues within 4Å: Chain A: D.517, I.518, G.519, P.559, G.560, C.561, S.562, K.563, T.564, L.565, E.617, N.660, I.692, G.721, V.725 Chain B: R.671, R.674 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.519, A:G.519, A:G.560, A:S.562, A:K.563, A:T.564, A:L.565, A:E.617, B:R.674 Salt bridges: A:K.563, B:R.671, B:R.671 AGS.3: 18 residues within 4Å: Chain B: A.246, V.247, G.248, P.288, G.289, T.290, G.291, K.292, T.293, M.294, N.390, I.422, Q.426, G.454, T.458 Chain C: D.375, R.401, R.404 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:A.246, B:G.248, B:G.289, B:G.289, B:T.290, B:T.290, B:G.291, B:K.292, B:K.292, B:T.293, B:T.293, B:M.294, C:R.401, C:R.404 Salt bridges: B:K.292, C:R.401, C:R.401 AGS.4: 19 residues within 4Å: Chain B: D.517, I.518, G.519, P.559, G.560, C.561, S.562, K.563, T.564, L.565, N.660, I.692, G.721, A.722, V.725 Chain C: D.645, A.668, R.671, R.674 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.519, B:G.519, B:G.560, B:K.563, B:K.563, B:T.564, B:T.564, B:L.565, B:N.660, C:D.645, C:R.674 Salt bridges: B:K.563, C:R.671, C:R.671 AGS.5: 19 residues within 4Å: Chain C: A.246, V.247, G.248, P.288, G.289, T.290, G.291, K.292, T.293, M.294, E.346, I.422, Q.426, G.454, A.455, T.458 Chain D: D.375, R.401, R.404 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.248, C:G.248, C:G.289, C:G.291, C:K.292, C:T.293, C:T.293, C:T.293, C:T.293, C:M.294, C:Q.426, D:D.375, D:R.401 Salt bridges: C:K.292, C:K.292, D:R.401, D:R.401, D:R.404 AGS.6: 15 residues within 4Å: Chain C: I.518, G.519, P.559, G.560, C.561, S.562, K.563, T.564, L.565, I.692, V.725 Chain D: D.645, A.668, R.671, R.674 16 PLIP interactions: 4 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:D.645, D:R.674, C:G.519, C:G.519, C:G.560, C:C.561, C:C.561, C:S.562, C:K.563, C:T.564, C:T.564, C:L.565, C:E.617 Salt bridges: D:R.671, D:R.671, C:K.563 AGS.7: 13 residues within 4Å: Chain D: G.248, G.289, T.290, G.291, K.292, T.293, D.345, N.390, I.422, Q.426, G.454, A.455, T.458 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.248, D:G.248, D:G.289, D:T.290, D:G.291, D:K.292, D:K.292, D:T.293, D:T.293, D:N.390 Salt bridges: D:K.292 AGS.8: 15 residues within 4Å: Chain D: D.517, I.518, G.519, P.559, G.560, C.561, S.562, K.563, T.564, L.565, D.616, N.660, G.721, A.722, V.725 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.519, D:G.519, D:G.560, D:C.561, D:K.563, D:T.564, D:T.564, D:L.565, D:D.616 Salt bridges: D:K.563 AGS.9: 17 residues within 4Å: Chain E: A.246, V.247, G.248, P.288, G.289, T.290, G.291, K.292, T.293, M.294, N.390, I.422, V.453, G.454, A.455, T.458 Chain F: R.401 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:V.247, E:G.291, E:K.292, E:T.293, E:T.293, E:M.294, E:N.390, E:N.390, E:N.390, F:R.401, F:R.401 Salt bridges: F:R.401 AGS.10: 16 residues within 4Å: Chain F: A.246, V.247, G.248, P.287, P.288, G.289, T.290, G.291, K.292, T.293, M.294, N.390, I.422, G.454, A.455, T.458 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.248, F:G.289, F:T.290, F:G.291, F:K.292, F:K.292, F:T.293, F:T.293, F:T.293, F:M.294, F:N.390 Salt bridges: F:K.292 AGS.11: 16 residues within 4Å: Chain A: R.671, R.674 Chain F: I.518, G.519, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, D.616, E.617, I.692, G.721 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain F Hydrogen bonds: A:R.671, A:R.671, F:G.519, F:G.519, F:G.560, F:C.561, F:K.563, F:T.564, F:T.564, F:L.565 Salt bridges: A:R.671, A:R.671, A:R.674, F:K.563, F:K.563

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prattes, M. et al., Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-09-21

Peptides

ATPase family gene 2 protein: ABCDEF
peptide substrate: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATPase family gene 2 protein

peptide substrate

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