SMTL ID : 7z2b.1

P. berghei kinesin-8B motor domain in AMPPNP state bound to tubulin dimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

ANP.1: 16 residues within 4Å: Chain A: R.10, R.12, P.13, T.99, G.100, A.101, G.102, K.103, T.104, H.105, Y.110, S.211, L.244, A.245, G.246 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.100, A:A.101, A:G.102, A:G.102, A:K.103, A:K.103, A:T.104, A:T.104, A:H.105, A:Y.110, A:S.211, A:S.211, A:G.246 pi-Stacking: A:H.105, A:H.105

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.104, S.211, D.243 Ligands: ANP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.104, A:S.211 MG.4: 3 residues within 4Å: Chain B: Q.11 Chain C: K.252 Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: Q.11 Ligands: G2P.5 No protein-ligand interaction detected (PLIP)

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

GTP.3: 25 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, I.16, D.89, A.90, A.91, N.92, S.131, G.133, G.134, G.135, T.136, G.137, I.162, T.170, N.197, Y.215, L.218, N.219, I.222 Chain C: L.246, K.252 Ligands: MG.4 21 PLIP interactions: 18 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:T.136, B:G.137, B:N.197, B:N.197, B:Y.215, 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

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

G2P.5: 23 residues within 4Å: Chain C: G.10, Q.11, C.12, Q.15, I.16, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, D.177, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.6 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:T.143, C:G.144, C:N.204, C:Y.222, 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

2022-11-16

Peptides

Kinesin-8, putative: 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-8, putative

Detyrosinated tubulin alpha-1B chain

Tubulin beta chain

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