SMTL ID : 6pdy.1

Msp1-substrate complex in open conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain B: I.85, G.86, L.88, P.128, G.129, C.130, G.131, K.132, T.133, M.134, Q.261, I.265, G.293, S.294, K.297 Chain C: D.214, R.246 Ligands: BEF.2, MG.3 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.86, B:G.129, B:G.131, B:K.132, B:T.133, B:T.133, B:T.133, B:M.134, B:Q.261, B:S.294 Salt bridges: B:K.132, C:R.246, C:R.246 ADP.4: 18 residues within 4Å: Chain C: I.85, G.86, P.127, P.128, G.129, C.130, G.131, K.132, T.133, M.134, I.265, G.293, S.294, K.297 Chain D: D.214, R.246 Ligands: BEF.5, MG.6 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.86, C:G.86, C:P.127, C:G.129, C:C.130, C:G.131, C:K.132, C:T.133, C:T.133, C:M.134, C:K.297, D:D.214 Salt bridges: C:K.132, D:R.246, D:R.246 ADP.7: 16 residues within 4Å: Chain D: I.85, G.86, L.88, P.128, G.129, C.130, G.131, K.132, T.133, M.134, I.265, G.293, S.294, K.297 Chain E: R.246 Ligands: BEF.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.86, D:G.86, D:G.129, D:C.130, D:G.131, D:K.132, D:T.133, D:T.133, D:M.134, D:K.297 Salt bridges: D:K.132, E:R.246, E:R.246 ADP.10: 18 residues within 4Å: Chain E: D.84, I.85, G.86, P.128, G.129, C.130, G.131, K.132, T.133, M.134, I.265, L.268, G.293, S.294, K.297 Chain F: R.246 Ligands: MG.11, BEF.12 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.86, E:G.86, E:G.129, E:C.130, E:G.131, E:K.132, E:T.133, E:T.133, E:T.133, E:M.134, E:K.297 Salt bridges: E:K.132, F:R.246, F:R.246 ADP.13: 16 residues within 4Å: Chain A: D.214, R.246, R.247 Chain F: G.86, P.128, G.129, C.130, G.131, K.132, T.133, M.134, N.235, I.265, G.293, S.294, K.297 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:G.86, F:G.86, F:K.132, F:T.133, F:T.133, F:M.134, F:N.235, F:K.297, A:D.214, A:R.247 Salt bridges: F:K.132, F:K.132, A:R.246

4 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 8 residues within 4Å: Chain B: P.128, K.132, T.133, E.186 Chain C: R.246, R.247 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 8 residues within 4Å: Chain C: K.132, T.133, D.185, E.186 Chain D: R.246, R.247 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) BEF.8: 9 residues within 4Å: Chain D: K.132, T.133, D.185 Chain E: M.210, D.214, R.246, R.247 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP) BEF.12: 7 residues within 4Å: Chain E: K.132, T.133, D.185, E.186 Chain F: R.247 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain B: T.133, D.185, E.186 Ligands: ADP.1, BEF.2 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.185, B:D.185 MG.6: 4 residues within 4Å: Chain C: T.133 Chain D: R.246 Ligands: ADP.4, BEF.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.133 MG.9: 5 residues within 4Å: Chain D: T.133, D.185, A.233 Chain E: M.210 Ligands: BEF.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.133, D:D.185, D:D.185 MG.11: 4 residues within 4Å: Chain E: T.133, D.185 Ligands: ADP.10, BEF.12 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.133, E:D.185, E:D.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Structure of the AAA protein Msp1 reveals mechanism of mislocalized membrane protein extraction. Elife (2020)

Release Date

2020-02-12

Peptides

Membrane-spanning ATPase-like protein: ABCDEF
Unknown E. coli peptide: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
A

C
B

D
C

E
D

F
E

G
G

Membrane-spanning ATPase-like protein

Unknown E. coli peptide

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