SMTL ID : 2hxh.1

KIF1A head-microtubule complex structure in adp-form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: Q.11, D.69, E.71 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: S.120, S.230 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.120

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

GTP.2: 22 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain B: L.246, K.252 Ligands: MG.1 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.100, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:T.179, A:T.179, A:E.183, A:N.206, A:Y.224, A:N.228, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252

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

GDP.3: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:T.143, B:D.177, B:E.181, B:N.204, B:Y.222, B:N.226, B:N.226, B:N.226

1 x TA1: TAXOL(Non-covalent)

TA1.4: 19 residues within 4Å: Chain B: E.22, V.23, D.26, E.27, L.215, D.224, H.227, L.228, A.231, S.234, F.270, P.272, L.273, T.274, S.275, R.276, P.358, R.359, G.360 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.23, B:D.26, B:L.215, B:H.227, B:L.228, B:F.270, B:F.270, B:F.270, B:P.358 Hydrogen bonds: B:T.274, B:P.358, B:G.360 pi-Stacking: B:H.227

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

ADP.6: 15 residues within 4Å: Chain C: R.27, R.29, P.30, S.74, Y.83, Q.114, T.115, G.116, A.117, G.118, K.119, S.120, Y.121, K.126 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.83, C:Y.83, C:Q.114, C:G.116, C:A.117, C:G.118, C:K.119, C:S.120, C:Y.121, C:K.126 Salt bridges: C:K.119 pi-Stacking: C:Y.121, C:Y.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kikkawa, M. et al., High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations. Embo J. (2006)

Release Date

2006-10-10

Peptides

Tubulin alpha chain: A
Tubulin beta chain: B
Kinesin-like protein KIF1A: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Tubulin alpha chain

Tubulin beta chain

Kinesin-like protein KIF1A

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