SMTL ID : 7z2a.1

P. berghei kinesin-8B motor domain in no nucleotide state bound to tubulin dimer

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, D.89, A.90, A.91, N.92, S.131, G.134, G.135, T.136, G.137, I.162, T.170, E.174, N.197, Y.215, N.219, I.222 Chain B: K.252 Ligands: MG.2 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:A.90, A:A.91, A:N.92, A:S.131, A:G.135, A:T.136, A:G.137, A:E.174, A:N.197, A:N.197, A:N.219, A:N.219 pi-Stacking: A:Y.215, A:Y.215 Salt bridges: B:K.252, B:K.252, B:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, E.62 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: Q.11 Ligands: G2P.3 No protein-ligand interaction detected (PLIP)

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

G2P.3: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, A.97, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:Q.15, B:A.97, B:G.98, B:N.99, B:N.99, B:S.138, B:G.142, B:T.143, B:G.144, B:D.177, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, T. et al., Mechanochemical tuning of a kinesin motor essential for malaria parasite transmission. Nat Commun (2022)

Release Date

2022-10-19

Peptides

Detyrosinated tubulin alpha-1B chain: A
Tubulin beta chain: B
Kinesin-8, putative: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
K

Detyrosinated tubulin alpha-1B chain

Tubulin beta chain

Kinesin-8, putative

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