SMTL ID : 6ugd.1

Katanin hexamer in the spiral conformation in complex with substrate

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: D.212, I.213, I.214, M.216, P.253, G.254, T.255, G.256, K.257, T.258, L.259, Q.311, A.417 Chain B: R.369, R.370 Ligands: MG.2 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Salt bridges: B:R.369, B:R.370 Hydrogen bonds: A:I.214, A:G.215, A:K.257, A:T.258, A:L.259, A:Q.311 ATP.3: 14 residues within 4Å: Chain B: I.213, I.214, P.253, G.254, T.255, G.256, K.257, T.258, L.259, N.358, A.417 Chain C: R.369, R.370 Ligands: MG.4 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:I.214, B:I.214, B:G.254, B:T.255, B:G.256, B:K.257, B:T.258, B:T.258, B:T.258, B:N.358 Salt bridges: B:K.257, B:K.257, C:R.369, C:R.369, C:R.369, C:R.370 ATP.5: 17 residues within 4Å: Chain C: I.213, I.214, P.253, G.254, T.255, G.256, K.257, T.258, L.259, Q.311, N.358, L.388, K.391, V.420 Chain D: R.369, R.370 Ligands: MG.6 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:I.214, C:I.214, C:G.256, C:K.257, C:T.258, C:L.259, C:Q.311, C:N.358, C:N.358, C:K.391, D:R.370 Salt bridges: C:K.257, C:K.257, D:R.369, D:R.369, D:R.370 ATP.7: 15 residues within 4Å: Chain D: D.212, I.213, I.214, P.253, G.254, T.255, G.256, K.257, T.258, L.259, L.388, A.417 Chain E: R.369, R.370 Ligands: MG.8 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain D Salt bridges: E:R.369, E:R.369, E:R.369, E:R.370, D:K.257 Hydrogen bonds: D:I.214, D:I.214, D:G.254, D:T.255, D:G.256, D:K.257, D:T.258, D:L.259 ATP.9: 15 residues within 4Å: Chain E: D.212, I.213, I.214, P.253, T.255, G.256, K.257, T.258, L.259, N.358, G.416, A.417 Chain F: R.369, R.370 Ligands: MG.10 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:I.214, E:I.214, E:K.257, E:T.258, E:L.259, E:N.358, E:N.358 Salt bridges: E:K.257, F:R.369, F:R.370, F:R.370 ATP.11: 13 residues within 4Å: Chain F: D.212, I.213, I.214, P.253, G.254, T.255, G.256, K.257, T.258, L.259, N.358, G.416, A.417 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:I.214, F:I.214, F:G.254, F:T.255, F:G.256, F:K.257, F:T.258, F:L.259 Salt bridges: F:K.257

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.258, D.310 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.258 MG.4: 3 residues within 4Å: Chain B: T.258 Chain C: R.370 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.258 MG.6: 3 residues within 4Å: Chain C: T.258, D.310 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.258 MG.8: 3 residues within 4Å: Chain D: T.258 Chain E: R.370 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.258 MG.10: 3 residues within 4Å: Chain E: T.258, D.310 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zehr, E.A. et al., Katanin Grips the beta-Tubulin Tail through an Electropositive Double Spiral to Sever Microtubules. Dev.Cell (2020)

Release Date

2019-10-09

Peptides

Meiotic spindle formation protein mei-1: 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

Meiotic spindle formation protein mei-1

Polyglutamate peptide

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