SMTL ID : 9l7m.1

Nucleotide-free kinesin-1 motor domain bound to the microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 20 residues within 4Å: Chain A: G.10, Q.11, A.12, E.71, A.99, A.100, N.101, 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.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:E.71, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:T.145, A:G.146, A:T.179, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 pi-Cation interactions: A:Y.224 GTP.3: 15 residues within 4Å: Chain A: E.254 Chain B: G.10, Q.11, C.12, E.69, A.97, N.99, S.138, G.141, G.142, T.143, N.204, Y.222, N.226 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:E.69, B:A.97, B:N.99, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:N.204, B:N.226, B:N.226, B:N.226 pi-Cation interactions: B:Y.222 GTP.5: 21 residues within 4Å: Chain B: K.252 Chain C: G.10, Q.11, A.12, E.71, A.99, A.100, N.101, 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.6 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:E.71, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:T.145, C:G.146, C:T.179, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 pi-Cation interactions: C:Y.224 Salt bridges: B:K.252 GTP.7: 15 residues within 4Å: Chain C: E.254 Chain D: G.10, Q.11, C.12, E.69, A.97, N.99, S.138, G.141, G.142, T.143, N.204, Y.222, N.226 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:E.69, D:A.97, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:N.204, D:N.226, D:N.226, D:N.226 pi-Cation interactions: D:Y.222

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.71 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.71, A:E.71 MG.4: 2 residues within 4Å: Chain B: E.69 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.69 MG.6: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.71, C:E.71 MG.8: 2 residues within 4Å: Chain D: E.69 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makino, T. et al., Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping. Biorxiv (2024)

Release Date

2025-04-23

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD
Kinesin-1 heavy chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
K

Tubulin alpha-1B chain

Tubulin beta chain

Kinesin-1 heavy chain

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