SMTL ID : 9gnq.1

Microtubule-associated Kif5B IAK tail mutant bound to ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

GDP.1: 14 residues within 4Å: Chain A: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.11, A:C.12, A:S.138, A:G.142, A:T.143, A:G.144, A:D.177, A:E.181, A:N.204, A:Y.222, A:N.226, A:N.226, A:N.226 pi-Stacking: A:Y.222 pi-Cation interactions: A:Y.222

1 x TA1: TAXOL(Non-covalent)

TA1.2: 17 residues within 4Å: Chain A: V.23, D.26, L.215, D.224, H.227, L.228, A.231, S.234, P.272, L.273, T.274, R.276, Q.279, P.358, R.359, G.360, L.361 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.23, A:V.23, A:D.26, A:H.227, A:L.228, A:A.231, A:L.361 Hydrogen bonds: A:T.274, A:Q.279, A:R.359 pi-Cation interactions: A:H.227

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

GTP.3: 19 residues within 4Å: Chain A: K.252 Chain B: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, E.183, N.206, Y.224, N.228 Ligands: MG.4 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.11, B:A.12, B:A.99, B:A.100, B:N.101, B:S.140, B:G.144, B:T.145, B:G.146, B:T.179, B:E.183, B:N.206, B:Y.224, B:N.228, B:N.228 pi-Stacking: B:Y.224 pi-Cation interactions: B:Y.224 Salt bridges: A:K.252, A:K.252, A:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.252 Chain B: E.71 Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

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

ADP.5: 12 residues within 4Å: Chain C: R.14, F.15, R.16, P.17, Q.86, T.87, S.88, S.89, G.90, K.91, T.92, H.93 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.14, C:Q.86, C:S.88, C:S.89, C:G.90, C:K.91, C:T.92, C:T.92, C:H.93 pi-Cation interactions: C:H.93, C:H.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atherton, J. et al., Microtubule association induces a Mg-free apo-like ADP pre-release conformation in kinesin-1 that is unaffected by its autoinhibitory tail. Biorxiv (2024)

Release Date

2024-11-20

Peptides

Tubulin beta chain: A
Tubulin alpha-1B chain: B
Kinesin-1 heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
K

Tubulin beta chain

Tubulin alpha-1B chain

Kinesin-1 heavy chain

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