SMTL ID : 3j6h.1

Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: Q.10 Chain B: Q.244 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain B: Q.10, D.66, E.68, T.71 Ligands: G2P.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.68, B:T.71

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.2: 23 residues within 4Å: Chain A: N.100, S.139, G.141, G.142, G.143, A.173, V.176, S.177, T.178, A.179, N.205, E.206, I.208, Y.209, C.212, P.221, T.222, Y.223, N.225, L.226, L.229 Chain B: L.245 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.100, A:S.139, A:G.143, A:T.178, A:T.178, A:A.179, A:I.208, A:Y.209, A:N.225, A:L.226 pi-Stacking: A:Y.209, A:Y.209

1 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Covalent)

G2P.4: 22 residues within 4Å: Chain B: A.8, G.9, Q.10, C.11, G.12, Q.14, D.66, E.68, A.96, S.137, G.139, G.140, G.141, T.142, G.143, D.176, E.180, N.203, Y.221, L.224, N.225 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.10, B:C.11, B:G.12, B:E.68, B:A.96, B:S.137, B:G.141, B:T.142, B:D.176, B:D.176, B:E.180, B:N.203, B:N.203, B:N.225, B:N.225

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain C: T.88, S.89, S.90, G.91, K.92, T.93 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.89, C:S.90, C:G.91, C:K.92, C:T.93 Salt bridges: C:K.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morikawa, M. et al., X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding. Embo J. (2015)

Release Date

2015-04-01

Peptides

Tubulin alpha-1A chain: A
Tubulin beta chain: B
Kinesin heavy chain isoform 5C: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
K

Tubulin alpha-1A chain

Tubulin beta chain

Kinesin heavy chain isoform 5C

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