SMTL ID : 7t3i.1

CryoEM structure of the Rix7 D2 Walker B mutant

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: H.502, G.504, L.506, P.543, P.544, G.545, C.546, G.547, K.548, T.549, L.550, Q.602, N.645, L.681, G.733, A.734 Chain B: D.630, R.656, R.659 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain A Salt bridges: B:R.656, B:R.656, B:R.656, B:R.659, A:K.548, A:K.548 Hydrogen bonds: A:G.504, A:G.504, A:P.543, A:G.545, A:C.546, A:G.547, A:K.548, A:T.549, A:T.549, A:L.550, A:Q.602, A:N.645, A:A.734 ATP.2: 16 residues within 4Å: Chain A: D.203, I.204, A.205, G.246, C.247, G.248, K.249, T.250, T.251, I.380, G.408, S.409 Chain B: D.331, R.334, R.361, R.362 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.205, A:A.205, A:G.246, A:G.248, A:K.249, A:T.250, A:T.250, A:T.250, A:T.251 Salt bridges: A:K.249, A:K.249, B:R.361, B:R.362, B:R.362 ATP.3: 18 residues within 4Å: Chain B: D.203, A.205, S.245, G.246, C.247, G.248, K.249, T.250, T.251, I.380, L.384, G.408, S.409, Q.412 Chain C: M.327, D.331, R.361, R.362 16 PLIP interactions: 5 interactions with chain C, 11 interactions with chain B Salt bridges: C:R.361, C:R.361, C:R.361, C:R.362, C:R.362, B:K.249, B:K.249 Hydrogen bonds: B:A.205, B:A.205, B:G.246, B:G.248, B:K.249, B:T.250, B:T.250, B:T.250, B:T.251 ATP.4: 19 residues within 4Å: Chain B: H.502, V.503, G.504, L.506, P.544, G.545, C.546, G.547, K.548, T.549, L.550, Q.602, N.645, I.677, G.733, A.734 Chain C: D.630, R.656, R.659 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.504, B:G.504, B:G.545, B:C.546, B:G.547, B:K.548, B:T.549, B:T.549, B:T.549, B:L.550 Salt bridges: C:R.656, C:R.656, C:R.656, C:R.659 ATP.5: 18 residues within 4Å: Chain C: H.502, V.503, G.504, P.543, P.544, G.545, C.546, G.547, K.548, T.549, L.550, N.645, I.677, G.733, A.734 Chain D: D.630, R.656, R.659 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.504, C:G.504, C:P.543, C:G.545, C:C.546, C:G.547, C:K.548, C:T.549, C:T.549, C:T.549, C:L.550, C:N.645 Salt bridges: C:K.548, C:K.548, D:R.656, D:R.656, D:R.656, D:R.659 ATP.6: 20 residues within 4Å: Chain C: D.203, I.204, A.205, S.245, G.246, C.247, G.248, K.249, T.250, T.251, D.302, E.303, I.380, G.408, S.409 Chain D: M.327, D.331, R.334, R.361, R.362 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:A.205, C:A.205, C:G.246, C:C.247, C:G.248, C:K.249, C:T.250, C:T.250, C:T.250, C:T.251, C:D.302, D:R.334 Salt bridges: C:K.249, C:K.249, D:R.361, D:R.361, D:R.362 ATP.7: 18 residues within 4Å: Chain D: H.502, V.503, G.504, P.544, G.545, C.546, G.547, K.548, T.549, L.550, Q.602, N.645, L.681, G.733, A.734 Chain E: D.630, R.656, R.659 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.504, D:G.504, D:G.545, D:C.546, D:G.547, D:G.547, D:K.548, D:T.549, D:T.549, D:L.550, D:Q.602, D:N.645, D:N.645 Salt bridges: D:K.548, D:K.548, E:R.656, E:R.656, E:R.659 ATP.8: 17 residues within 4Å: Chain D: D.203, I.204, A.205, P.244, S.245, G.246, C.247, G.248, K.249, T.250, T.251, N.350, I.380, G.408, S.409 Chain E: R.334, R.362 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:A.205, D:A.205, D:G.246, D:C.247, D:G.248, D:K.249, D:T.250, D:T.250, D:T.250, D:T.251, D:N.350, E:R.334 Salt bridges: D:K.249, D:K.249, E:R.362, E:R.362

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 6 residues within 4Å: Chain E: G.246, C.247, G.248, K.249, T.250, T.251 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.246, E:G.248, E:G.248, E:K.249, E:T.250, E:T.250, E:T.250, E:T.251 Salt bridges: E:K.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kocaman, S. et al., Communication network within the essential AAA-ATPase Rix7 drives ribosome assembly. Pnas Nexus (2022)

Release Date

2022-03-02

Peptides

Rix7: ABCDEF
substrate peptide: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Rix7

substrate peptide

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