SMTL ID : 6pek.1

Structure of Spastin Hexamer (Subunit A-E) in complex with substrate peptide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-1-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: A.227, P.266, G.267, N.268, G.269, K.270, T.271, M.272, L.399, G.428, S.429, T.432 Chain B: D.352, R.380, R.381 Ligands: BEF.2, MG.3 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.227, A:A.227, A:G.267, A:N.268, A:G.269, A:K.270, A:T.271, A:M.272, A:G.428, A:T.432 Salt bridges: B:R.380, B:R.380, B:R.381 ADP.4: 17 residues within 4Å: Chain B: A.227, P.266, G.267, N.268, G.269, K.270, T.271, M.272, L.399, G.428, S.429, T.432 Chain C: D.352, R.380, R.381 Ligands: BEF.5, MG.6 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.227, B:G.267, B:N.268, B:G.269, B:T.271, B:M.272, B:S.429, B:T.432 Salt bridges: C:R.380, C:R.380 ADP.7: 18 residues within 4Å: Chain C: D.225, I.226, A.227, G.267, N.268, G.269, K.270, T.271, M.272, L.399, G.428, S.429, T.432 Chain D: D.352, R.380, R.381 Ligands: BEF.8, MG.9 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:A.227, C:A.227, C:G.267, C:N.268, C:G.269, C:T.271, C:M.272, C:T.432, D:D.352 Salt bridges: D:R.380, D:R.380, D:R.381 ADP.10: 15 residues within 4Å: Chain D: D.225, I.226, A.227, G.267, N.268, G.269, K.270, T.271, M.272, G.428, T.432 Chain E: D.352, R.381 Ligands: BEF.11, MG.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:A.227, D:G.267, D:N.268, D:N.268, D:G.269, D:K.270, D:T.271, D:T.271, D:M.272, D:T.432 Salt bridges: D:K.270 ADP.13: 11 residues within 4Å: Chain E: D.225, I.226, P.266, G.267, N.268, G.269, K.270, T.271, M.272, L.399, G.428 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.267, E:N.268, E:G.269, E:K.270, E:T.271, E:G.428 Salt bridges: E:K.270

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

BEF.2: 9 residues within 4Å: Chain A: P.266, G.267, K.270, D.323, N.369 Chain B: R.380, R.381 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 8 residues within 4Å: Chain B: P.266, G.267, K.270, N.369 Chain C: R.380, R.381 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) BEF.8: 10 residues within 4Å: Chain C: P.265, P.266, G.267, N.268, K.270, N.369 Chain D: R.380, R.381 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP) BEF.11: 9 residues within 4Å: Chain D: P.266, G.267, K.270, T.271, N.369 Chain E: R.380, R.381 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.271, D.323 Chain B: R.381 Ligands: ADP.1, BEF.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.271, A:D.323 MG.6: 4 residues within 4Å: Chain B: T.271, D.323 Ligands: ADP.4, BEF.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.271, B:D.323 MG.9: 4 residues within 4Å: Chain C: T.271, D.323 Ligands: ADP.7, BEF.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.271 MG.12: 4 residues within 4Å: Chain D: T.271, D.323 Ligands: ADP.10, BEF.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, H. et al., Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation. J.Biol.Chem. (2020)

Release Date

2019-12-04

Peptides

Spastin: ABCDE
substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

Spastin

substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU

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