SMTL ID : 7z2c.1

P. falciparum kinesin-8B motor domain in no nucleotide 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 B: 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 C: K.252 Ligands: MG.2 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Q.11, B:A.12, B:Q.15, B:A.90, B:A.91, B:N.92, B:S.131, B:G.135, B:T.136, B:G.137, B:E.174, B:N.197, B:N.197, B:N.219, B:N.219 pi-Stacking: B:Y.215, B:Y.215 Salt bridges: C:K.252, C:K.252, C:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: Q.11, E.62 Chain C: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain C: 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 C: 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 C Hydrogen bonds: C:Q.11, C:C.12, C:Q.15, C:A.97, C:G.98, C:N.99, C:N.99, C:S.138, C:G.142, C:T.143, C:G.144, C:D.177, C:E.181, C:N.204, C:N.226, C:N.226, C:N.226 pi-Stacking: C:Y.222, C: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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
A

C
H

Kinesin-like protein

Detyrosinated tubulin alpha-1B chain

Tubulin beta chain

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