SMTL ID : 6vpo.1

Cryo-EM structure of microtubule-bound KLP61F motor domain in the AMPPNP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1: 22 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, N.206, Y.224, N.228 Chain B: L.246, K.252 Ligands: MG.2 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:E.71, A:N.101, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:T.145, A:T.145, A:G.146, A:T.179, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224 pi-Cation interactions: A:Y.224 Salt bridges: B:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.101 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP)

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, L.207, Y.222, N.226 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:T.143, B:T.143, B:G.144, B:E.181, B:N.204, B:Y.222, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222

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

ANP.4: 13 residues within 4Å: Chain C: R.25, P.28, Q.104, G.106, T.107, G.108, K.109, T.110, H.111, N.225, Q.227, S.228, S.229 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:R.25, C:G.106, C:T.107, C:G.108, C:K.109, C:K.109, C:K.109, C:K.109, C:T.110, C:T.110, C:T.110, C:H.111, C:N.225, C:S.229, C:S.229, C:S.229, C:G.264 pi-Stacking: C:H.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bodrug, T. et al., The kinesin-5 tail domain directly modulates the mechanochemical cycle of the motor domain for anti-parallel microtubule sliding. Elife (2020)

Release Date

2020-02-19

Peptides

Tubulin alpha-1A chain: A
Tubulin beta chain: B
Kinesin-like protein Klp61F: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Tubulin alpha-1A chain

Tubulin beta chain

Kinesin-like protein Klp61F

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