SMTL ID : 6ta4.1

Human kinesin-5 motor domain in the AMPPNP state bound to microtubules

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

G2P.1: 16 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, L.68, N.99, S.138, G.141, T.143, G.144, V.169, E.181, L.207, Y.222, N.226 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.11, A:C.12, A:Q.15, A:S.138, A:T.143, A:T.143, A:G.144, A:E.181, A:N.226

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, L.68 Ligands: G2P.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: Q.11, E.71 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71 MG.6: 6 residues within 4Å: Chain C: T.134, Y.253, S.254, S.255, D.287 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.287

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 28 residues within 4Å: Chain A: L.246, N.247, D.249, K.252 Chain B: G.10, Q.11, A.12, G.13, Q.15, I.16, E.71, A.99, A.100, N.101, F.138, S.140, G.142, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Ligands: MG.4 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:G.13, B:Q.15, B:N.101, B:N.101, B:S.140, B:G.142, B:G.143, B:G.144, B:T.145, B:G.146, B:T.179, B:E.183, B:N.206, A:D.249 Salt bridges: A:K.252

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.5: 21 residues within 4Å: Chain C: R.46, R.48, P.49, Q.100, T.129, G.130, T.131, G.132, K.133, T.134, F.135, N.251, Y.253, S.254, S.255, R.256, D.287, L.288, A.289, G.290 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:R.46, C:R.46, C:Q.100, C:T.129, C:G.130, C:T.131, C:G.132, C:K.133, C:T.134, C:F.135, C:N.251, C:S.255, C:R.256, C:R.256, C:G.290 pi-Stacking: C:F.135, C:F.135 pi-Cation interactions: C:R.48

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

2020-03-04

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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