SMTL ID : 6p07.1

Spastin hexamer in complex with substrate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: D.220, I.221, A.222, P.260, P.261, G.262, N.263, G.264, K.265, T.266, L.267, N.365, L.395, G.424, S.425 Chain B: A.373, R.376, R.377 Ligands: MG.2 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.220, A:A.222, A:G.262, A:N.263, A:G.264, A:K.265, A:T.266, A:T.266, A:L.267, A:Q.319, A:N.365, B:R.376 Salt bridges: A:K.265, A:K.265, A:K.265, B:R.376, B:R.376, B:R.376, B:R.377, B:R.377 ATP.3: 19 residues within 4Å: Chain B: D.220, I.221, A.222, P.261, G.262, N.263, G.264, K.265, T.266, L.267, Q.319, N.365, L.395, G.424, T.428 Chain C: A.373, R.376, R.377 Ligands: MG.4 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:A.222, B:A.222, B:G.262, B:G.264, B:K.265, B:T.266, B:L.267, B:Q.319, B:N.365 Salt bridges: B:K.265, B:K.265, C:R.376, C:R.376, C:R.376, C:R.377 ATP.5: 19 residues within 4Å: Chain C: D.220, I.221, A.222, P.261, G.262, N.263, G.264, K.265, T.266, L.267, Q.319, N.365, L.395, G.424, S.425, T.428 Chain D: R.376, R.377 Ligands: MG.6 15 PLIP interactions: 4 interactions with chain D, 11 interactions with chain C Salt bridges: D:R.376, D:R.376, D:R.376, D:R.377, C:K.265, C:K.265 Hydrogen bonds: C:A.222, C:A.222, C:G.262, C:G.264, C:K.265, C:T.266, C:L.267, C:Q.319, C:N.365 ATP.7: 21 residues within 4Å: Chain D: D.220, I.221, A.222, P.261, G.262, N.263, G.264, K.265, T.266, L.267, D.318, Q.319, N.365, L.395, G.424, S.425, T.428 Chain E: A.373, R.376, R.377 Ligands: MG.8 17 PLIP interactions: 12 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:A.222, D:G.262, D:N.263, D:N.263, D:G.264, D:K.265, D:T.266, D:Q.319, D:N.365, D:N.365, E:R.376 Salt bridges: D:K.265, D:K.265, E:R.376, E:R.376, E:R.377, E:R.377 ATP.9: 19 residues within 4Å: Chain E: D.220, I.221, A.222, P.261, G.262, N.263, K.265, T.266, L.267, Q.319, N.365, L.395, S.425, T.428 Chain F: L.343, A.373, R.376, R.377 Ligands: MG.10 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:A.222, E:G.262, E:N.263, E:K.265, E:T.266, E:Q.319, E:Q.319, E:Q.319, E:N.365, E:T.428, F:R.376 Salt bridges: E:K.265, E:K.265, E:K.265, F:R.376, F:R.376, F:R.377, F:R.377 ATP.11: 16 residues within 4Å: Chain F: D.220, A.222, P.261, G.262, N.263, G.264, K.265, T.266, Q.319, N.365, L.395, G.424, S.425, T.428 Ligands: ADP.12, MG.13 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:A.222, F:A.222, F:G.262, F:K.265, F:T.266, F:Q.319, F:N.365, F:N.365, F:N.365 Salt bridges: F:K.265

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.266 Chain B: R.377 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.266 MG.4: 3 residues within 4Å: Chain B: T.266, D.318 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.266 MG.6: 4 residues within 4Å: Chain C: T.266, D.318, Q.319 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.266 MG.8: 5 residues within 4Å: Chain D: T.266, D.318 Chain E: D.347, R.377 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.266 MG.10: 5 residues within 4Å: Chain E: T.266, D.318 Chain F: D.347, R.377 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.266, E:D.318 MG.13: 3 residues within 4Å: Chain F: T.266 Ligands: ATP.11, ADP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.266

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

ADP.12: 15 residues within 4Å: Chain F: A.222, P.261, G.262, N.263, G.264, K.265, T.266, L.267, N.365, L.395, G.424, S.425, T.428 Ligands: ATP.11, MG.13 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:A.222, F:G.262, F:K.265, F:T.266, F:T.266, F:N.365 Salt bridges: F:K.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sandate, C.R. et al., An allosteric network in spastin couples multiple activities required for microtubule severing. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-06-12

Peptides

Spastin: ABCDEF
polyglutamate peptide: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Spastin

polyglutamate peptide