SMTL ID : 7us2.1

PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain hexamer bound to ATPgammaS, open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

AGS.1: 19 residues within 4Å: Chain A: H.220, I.221, I.222, S.257, G.258, I.259, G.260, K.261, T.262, E.263, D.328, Q.329, N.370, F.445, L.453, A.493, R.494, K.497 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:I.222, A:I.222, A:G.258, A:I.259, A:G.260, A:K.261, A:T.262, A:E.263, A:E.263, A:E.263, A:Q.329, A:N.370, A:R.494 Salt bridges: A:K.261, A:R.494 AGS.3: 24 residues within 4Å: Chain A: H.247, E.431, R.435 Chain B: H.220, I.221, I.222, S.256, S.257, G.258, I.259, G.260, K.261, T.262, E.263, Q.329, T.368, N.370, F.445, L.453, K.456, A.493, R.494, K.497 Ligands: MG.4 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:I.222, B:I.222, B:S.256, B:G.258, B:I.259, B:G.260, B:K.261, B:T.262, B:E.263, B:E.263, B:E.263, B:Q.329, B:N.370, B:R.494, A:H.247, A:E.431, A:E.431, A:R.435, A:R.435 Salt bridges: B:K.261, B:R.494 AGS.5: 23 residues within 4Å: Chain B: H.247, E.431, R.435 Chain C: H.220, I.221, I.222, S.256, S.257, G.258, I.259, G.260, K.261, T.262, E.263, Q.329, N.370, F.445, L.453, K.456, A.493, R.494, K.497 Ligands: MG.6 21 PLIP interactions: 4 interactions with chain B, 17 interactions with chain C Hydrogen bonds: B:H.247, B:E.431, B:R.435, B:R.435, C:I.222, C:I.222, C:S.256, C:G.258, C:I.259, C:G.260, C:K.261, C:K.261, C:T.262, C:E.263, C:E.263, C:E.263, C:N.370, C:R.494 Salt bridges: C:K.261, C:R.494, C:R.494 AGS.7: 23 residues within 4Å: Chain C: H.247, E.431, R.435 Chain D: H.220, I.221, I.222, S.256, S.257, G.258, I.259, G.260, K.261, T.262, E.263, Q.329, N.370, F.445, L.453, K.456, A.493, R.494, K.497 Ligands: MG.8 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:I.222, D:S.256, D:G.258, D:I.259, D:I.259, D:G.260, D:K.261, D:K.261, D:T.262, D:T.262, D:E.263, D:E.263, D:Q.329, D:N.370, D:N.370, D:R.494, C:H.247, C:R.435, C:R.435 Salt bridges: D:K.261, D:R.494, D:R.494 AGS.9: 23 residues within 4Å: Chain D: H.247, E.431, R.435 Chain E: H.220, I.221, I.222, S.256, S.257, G.258, I.259, G.260, K.261, T.262, E.263, Q.329, N.370, F.445, L.453, K.456, A.493, R.494, K.497 Ligands: MG.10 23 PLIP interactions: 17 interactions with chain E, 6 interactions with chain D Hydrogen bonds: E:I.222, E:I.222, E:S.256, E:G.258, E:I.259, E:G.260, E:K.261, E:K.261, E:T.262, E:E.263, E:E.263, E:Q.329, E:N.370, E:R.494, D:H.247, D:E.431, D:E.431, D:E.431, D:R.435, D:R.435 Salt bridges: E:K.261, E:R.494, E:R.494 AGS.11: 24 residues within 4Å: Chain E: H.247, E.431, R.435 Chain F: H.220, I.221, I.222, S.256, S.257, G.258, I.259, G.260, K.261, T.262, E.263, Q.329, T.368, N.370, F.445, L.453, K.456, A.493, R.494, K.497 Ligands: MG.12 23 PLIP interactions: 17 interactions with chain F, 6 interactions with chain E Hydrogen bonds: F:I.222, F:I.222, F:S.256, F:G.258, F:I.259, F:G.260, F:K.261, F:T.262, F:T.262, F:E.263, F:E.263, F:Q.329, F:N.370, F:R.494, E:H.247, E:E.431, E:E.431, E:E.431, E:R.435, E:R.435 Salt bridges: F:K.261, F:R.494, F:R.494

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.262 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.262 MG.4: 5 residues within 4Å: Chain B: T.262, D.328, Q.329, T.368 Ligands: AGS.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.262, B:D.328, B:D.328 MG.6: 3 residues within 4Å: Chain C: T.262, D.328 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.262 MG.8: 4 residues within 4Å: Chain C: R.435 Chain D: T.262, D.328 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.262 MG.10: 5 residues within 4Å: Chain D: D.346, R.435 Chain E: T.262, D.328 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.262 MG.12: 5 residues within 4Å: Chain E: R.435 Chain F: T.262, Q.329, R.494 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, A. et al., Dodecamer assembly of a metazoan AAA + chaperone couples substrate extraction to refolding. Sci Adv (2023)

Release Date

2023-04-26

Peptides

Caseinolytic peptidase B protein homolog: ABCDEF
Substrate: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
P

Caseinolytic peptidase B protein homolog

Substrate

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