SMTL ID : 6ta3.1

Human kinesin-5 motor domain in the GSK-1 state bound to microtubules (Conformation 1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Covalent)(Non-covalent)

G2P.1: 19 residues within 4Å: Chain A: G.10, Q.11, C.12, L.68, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, E.181, N.204, L.207, Y.222, L.225, N.226 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.10, A:Q.11, A:Q.11, A:C.12, A:G.98, A:N.99, A:N.99, A:S.138, A:G.142, A:T.143, A:T.143, A:G.144, A:E.181, A:E.181, A:N.204, A:N.204, A:Y.222, A:N.226 pi-Stacking: A:Y.222, A:Y.222 pi-Cation interactions: A:Y.222 G2P.3: 23 residues within 4Å: Chain A: R.251, K.252 Chain B: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:Q.15, B:D.98, B:A.99, B:A.100, B:N.101, B:S.140, B:G.144, B:T.145, B:T.145, B:G.146, B:T.179, B:T.179, B:E.183, B:N.206, B:Y.224, B:N.228

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, L.68, N.99 Ligands: G2P.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: Q.11, E.71, D.98 Ligands: G2P.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71

1 x MZK: 6-[4-(trifluoromethyl)phenyl]-3,4-dihydro-1~{H}-quinolin-2-one(Non-covalent)

MZK.5: 14 residues within 4Å: Chain B: R.402, E.415 Chain C: Y.126, G.127, Q.128, L.314, G.318, T.322, E.367, S.370, T.371, E.373, Y.374, R.377 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:R.402, C:G.318, C:R.377, C:R.377 Hydrophobic interactions: C:Y.126, C:Y.126, C:L.314, C:E.373, C:Y.374 Halogen bonds: C:Q.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pena, A. et al., Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy. Structure (2020)

Release Date

2020-04-22

Peptides

Tubulin beta chain: A
Tubulin alpha-1B chain: B
Kinesin-like protein KIF11: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
K

Tubulin beta chain

Tubulin alpha-1B chain

Kinesin-like protein KIF11

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