SMTL ID : 7nba.1

Plasmodium falciparum kinesin-5 motor domain bound to AMPPNP, complexed with 14 protofilament microtubule.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, N.101, G.143, G.144, T.145, G.146, I.171, T.179, N.206, Y.224, L.227, N.228, I.231 Chain B: L.246, K.252 Ligands: MG.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:A.99, A:N.101, A:T.145, A:G.146, A:N.206, A:N.206, A:N.206, A:Y.224, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, E.71, V.74 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.71, A:E.71 MG.4: 4 residues within 4Å: Chain B: Q.11, E.69, T.72 Ligands: G2P.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.69, B:E.69 MG.6: 6 residues within 4Å: Chain C: T.113, K.264, S.265, S.266, D.298 Ligands: ANP.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.113, C:K.264, C:S.266

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

G2P.3: 20 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, E.69, N.99, S.138, 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.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:E.69, B:N.99, B:G.142, B:T.143, B:G.144, B:N.204, B:N.204, B:N.204, B:Y.222, B:N.226 pi-Stacking: B:Y.222

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

ANP.5: 17 residues within 4Å: Chain C: R.27, R.29, P.30, T.108, G.109, T.110, G.111, K.112, T.113, Y.114, N.262, K.263, K.264, S.265, S.266, G.301 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:R.27, C:T.108, C:T.108, C:G.109, C:T.110, C:G.111, C:G.111, C:K.112, C:T.113, C:Y.114, C:N.262, C:K.264, C:K.264, C:S.265, C:S.266 pi-Stacking: C:Y.114, C:Y.114 pi-Cation interactions: C:R.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, A.D. et al., Cryo-EM structure of a microtubule-bound parasite kinesin motor and implications for its mechanism and inhibition. J.Biol.Chem. (2021)

Release Date

2021-10-13

Peptides

Tubulin alpha-1B chain: A
Tubulin beta chain: B
Kinesin motor domain-containing protein,Kinesin motor domain-containing protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
K

Tubulin alpha-1B chain

Tubulin beta chain

Kinesin motor domain-containing protein,Kinesin motor domain-containing protein

Related Entries With Identical Sequence