SMTL ID : 8utv.1

KIF1A[1-393] P305L mutant ADP bound in complex with a microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

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

GTP.1: 19 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 GTP.3: 19 residues within 4Å: 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, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C 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:E.183, B:N.206, B:N.206, B:Y.224, B:N.228, B:N.228 pi-Stacking: B:Y.224, B:Y.224 Salt bridges: C:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.69, E.71, V.74 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.69, A:E.71 MG.4: 3 residues within 4Å: Chain B: D.69, E.71, V.74 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.69, B:E.71

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

GDP.5: 14 residues within 4Å: Chain C: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Q.11, C:C.12, C:S.138, C:G.142, C:G.144, C:D.177, C:E.181, C:N.204, C:Y.222, C:N.226, C:N.226 pi-Stacking: C:Y.222, C:Y.222

1 x TA1: TAXOL(Non-covalent)

TA1.6: 19 residues within 4Å: Chain C: V.23, D.26, E.27, L.215, D.224, H.227, A.231, S.234, F.270, P.272, L.273, T.274, R.276, Q.279, R.318, P.358, R.359, G.360, L.361 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.23, C:D.26, C:L.215, C:H.227, C:A.231, C:F.270, C:R.276 Hydrogen bonds: C:T.274, C:Q.279, C:R.359, C:G.360 pi-Cation interactions: C:H.227

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

ADP.7: 10 residues within 4Å: Chain D: R.13, P.14, N.16, S.58, Y.67, T.99, G.100, G.102, S.104, Y.105 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.58, D:S.58, D:G.100, D:S.104, D:T.213, D:T.213 pi-Stacking: D:Y.105, D:Y.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benoit, M.P.M.H. et al., Cryo-EM unveils kinesin KIF1A's processivity mechanism and the impact of its pathogenic variant P305L. Nat Commun (2024)

Release Date

2024-06-12

Peptides

Tubulin alpha-1B chain: AB
Tubulin beta-2B chain: C
Kinesin-like protein KIF1A: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

C
B

D
K

Tubulin alpha-1B chain

Tubulin beta-2B chain

Kinesin-like protein KIF1A

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