SMTL ID : 9di0.1

Cryo-EM structure of Kif18A bound to a microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 13 residues within 4Å: Chain A: R.23, R.25, P.26, T.121, G.122, A.123, G.124, K.125, T.126, H.127, T.230, R.233 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.23, A:R.25, A:G.122, A:A.123, A:G.124, A:K.125, A:T.126, A:T.126, A:H.127, A:T.230 Salt bridges: A:K.125, A:R.233 pi-Cation interactions: A:R.25, A:H.127

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.126, T.230, R.233 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.126 MG.6: 3 residues within 4Å: Chain B: K.252 Chain C: E.71 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.71

1 x TA1: TAXOL(Non-covalent)

TA1.3: 16 residues within 4Å: Chain B: D.26, L.215, L.217, D.224, H.227, L.228, A.231, S.234, F.270, P.272, L.273, T.274, R.276, Q.279, R.359, L.361 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:D.26, B:L.217, B:D.224, B:L.228, B:A.231, B:F.270, B:T.274 Hydrogen bonds: B:T.274, B:R.359 Salt bridges: B:R.276

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, S.138, G.140, G.141, T.143, G.144, D.177, T.178, N.204, Y.222, N.226 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.15, B:S.138, B:G.144, B:D.177, B:D.177, B:N.204, B:N.226, B:N.226, B:N.226 Salt bridges: B:E.69

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

GTP.5: 20 residues within 4Å: Chain B: L.246, K.252 Chain C: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, T.179, E.183, N.206, Y.224, N.228 Ligands: MG.6 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.11, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 pi-Cation interactions: C:Y.224 Salt bridges: B:K.252, B:K.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perez-Bertoldi, J.M. et al., HURP regulates Kif18A recruitment and activity to synergistically control microtubule dynamics. Nat Commun (2024)

Release Date

2025-07-16

Peptides

Kinesin-like protein KIF18A, Methylated-DNA--protein-cysteine methyltransferase chimera: A
Tubulin beta chain: B
Tubulin alpha-1B chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
K

C
L

Kinesin-like protein KIF18A, Methylated-DNA--protein-cysteine methyltransferase chimera

Tubulin beta chain

Tubulin alpha-1B chain

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