SMTL ID : 5xxt.1

GDP-microtubule complexed with nucleotide-free KIF5C

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-9-mer

Ligands

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

GTP.1: 22 residues within 4Å: Chain A: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain B: L.245, N.246, K.251 Ligands: MG.2 24 PLIP interactions: 5 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:N.246, A:Q.10, A:Q.10, A:A.11, A:D.97, A:A.98, A:A.99, A:N.100, A:S.139, A:G.143, A:T.144, A:T.144, A:G.145, A:E.182, A:N.205, A:N.227, A:N.227, A:N.227 Water bridges: B:A.247 Salt bridges: B:K.251, B:K.251, B:K.251 pi-Stacking: A:Y.223, A:Y.223 GTP.4: 22 residues within 4Å: Chain C: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain D: L.245, N.246, K.251 Ligands: MG.5 24 PLIP interactions: 19 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Q.10, C:Q.10, C:A.11, C:D.97, C:A.98, C:A.99, C:N.100, C:S.139, C:G.143, C:T.144, C:T.144, C:G.145, C:E.182, C:N.205, C:N.227, C:N.227, C:N.227, D:N.246 pi-Stacking: C:Y.223, C:Y.223 Water bridges: D:A.247 Salt bridges: D:K.251, D:K.251, D:K.251 GTP.7: 22 residues within 4Å: Chain E: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain F: L.245, N.246, K.251 Ligands: MG.8 24 PLIP interactions: 19 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:Q.10, E:Q.10, E:A.11, E:D.97, E:A.98, E:A.99, E:N.100, E:S.139, E:G.143, E:T.144, E:T.144, E:G.145, E:E.182, E:N.205, E:N.227, E:N.227, E:N.227, F:N.246 pi-Stacking: E:Y.223, E:Y.223 Water bridges: F:A.247 Salt bridges: F:K.251, F:K.251, F:K.251 GTP.10: 22 residues within 4Å: Chain G: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain H: L.245, N.246, K.251 Ligands: MG.11 24 PLIP interactions: 19 interactions with chain G, 5 interactions with chain H Hydrogen bonds: G:Q.10, G:Q.10, G:A.11, G:D.97, G:A.98, G:A.99, G:N.100, G:S.139, G:G.143, G:T.144, G:T.144, G:G.145, G:E.182, G:N.205, G:N.227, G:N.227, G:N.227, H:N.246 pi-Stacking: G:Y.223, G:Y.223 Water bridges: H:A.247 Salt bridges: H:K.251, H:K.251, H:K.251 GTP.13: 22 residues within 4Å: Chain I: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain J: L.245, N.246, K.251 Ligands: MG.14 24 PLIP interactions: 19 interactions with chain I, 5 interactions with chain J Hydrogen bonds: I:Q.10, I:Q.10, I:A.11, I:D.97, I:A.98, I:A.99, I:N.100, I:S.139, I:G.143, I:T.144, I:T.144, I:G.145, I:E.182, I:N.205, I:N.227, I:N.227, I:N.227, J:N.246 pi-Stacking: I:Y.223, I:Y.223 Water bridges: J:A.247 Salt bridges: J:K.251, J:K.251, J:K.251 GTP.16: 22 residues within 4Å: Chain K: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain L: L.245, N.246, K.251 Ligands: MG.17 24 PLIP interactions: 5 interactions with chain L, 19 interactions with chain K Hydrogen bonds: L:N.246, K:Q.10, K:Q.10, K:A.11, K:D.97, K:A.98, K:A.99, K:N.100, K:S.139, K:G.143, K:T.144, K:T.144, K:G.145, K:E.182, K:N.205, K:N.227, K:N.227, K:N.227 Water bridges: L:A.247 Salt bridges: L:K.251, L:K.251, L:K.251 pi-Stacking: K:Y.223, K:Y.223 GTP.19: 22 residues within 4Å: Chain M: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain N: L.245, N.246, K.251 Ligands: MG.20 24 PLIP interactions: 5 interactions with chain N, 19 interactions with chain M Hydrogen bonds: N:N.246, M:Q.10, M:Q.10, M:A.11, M:D.97, M:A.98, M:A.99, M:N.100, M:S.139, M:G.143, M:T.144, M:T.144, M:G.145, M:E.182, M:N.205, M:N.227, M:N.227, M:N.227 Water bridges: N:A.247 Salt bridges: N:K.251, N:K.251, N:K.251 pi-Stacking: M:Y.223, M:Y.223 GTP.22: 22 residues within 4Å: Chain O: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain P: L.245, N.246, K.251 Ligands: MG.23 24 PLIP interactions: 19 interactions with chain O, 5 interactions with chain P Hydrogen bonds: O:Q.10, O:Q.10, O:A.11, O:D.97, O:A.98, O:A.99, O:N.100, O:S.139, O:G.143, O:T.144, O:T.144, O:G.145, O:E.182, O:N.205, O:N.227, O:N.227, O:N.227, P:N.246 pi-Stacking: O:Y.223, O:Y.223 Water bridges: P:A.247 Salt bridges: P:K.251, P:K.251, P:K.251 GTP.25: 22 residues within 4Å: Chain Q: G.9, Q.10, Q.14, D.97, A.98, A.99, N.100, S.139, G.142, G.143, T.144, G.145, I.170, E.182, N.205, Y.223, N.227, I.230 Chain R: L.245, N.246, K.251 Ligands: MG.26 24 PLIP interactions: 19 interactions with chain Q, 5 interactions with chain R Hydrogen bonds: Q:Q.10, Q:Q.10, Q:A.11, Q:D.97, Q:A.98, Q:A.99, Q:N.100, Q:S.139, Q:G.143, Q:T.144, Q:T.144, Q:G.145, Q:E.182, Q:N.205, Q:N.227, Q:N.227, Q:N.227, R:N.246 pi-Stacking: Q:Y.223, Q:Y.223 Water bridges: R:A.247 Salt bridges: R:K.251, R:K.251, R:K.251

9 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: Q.10 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: Q.10 Ligands: GTP.4 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain E: Q.10 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain G: Q.10 Ligands: GTP.10 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain I: Q.10 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain K: Q.10 Ligands: GTP.16 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain M: Q.10 Ligands: GTP.19 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain O: Q.10 Ligands: GTP.22 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain Q: Q.10 Ligands: GTP.25 No protein-ligand interaction detected (PLIP)

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

GDP.3: 16 residues within 4Å: Chain B: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, D.176, E.180, N.203, Y.221, N.225 Chain I: L.247 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.10, B:C.11, B:N.98, B:S.137, B:G.141, B:T.142, B:T.142, B:G.143, B:E.180, B:N.203, B:N.225, B:N.225, B:N.225 pi-Stacking: B:Y.221, B:Y.221 GDP.6: 17 residues within 4Å: Chain D: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, V.174, D.176, E.180, N.203, Y.221, N.225 Chain G: L.247 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.10, D:C.11, D:N.98, D:S.137, D:G.141, D:T.142, D:T.142, D:G.143, D:E.180, D:N.203, D:N.225, D:N.225, D:N.225 pi-Stacking: D:Y.221, D:Y.221 GDP.9: 17 residues within 4Å: Chain F: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, V.174, D.176, E.180, N.203, Y.221, N.225 Chain K: L.247 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:Q.10, F:C.11, F:N.98, F:S.137, F:G.141, F:T.142, F:T.142, F:G.143, F:E.180, F:N.203, F:N.225, F:N.225, F:N.225 pi-Stacking: F:Y.221, F:Y.221 GDP.12: 15 residues within 4Å: Chain H: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, D.176, E.180, N.203, Y.221, N.225 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:Q.10, H:C.11, H:N.98, H:S.137, H:G.141, H:T.142, H:T.142, H:G.143, H:E.180, H:N.203, H:N.225, H:N.225, H:N.225 pi-Stacking: H:Y.221, H:Y.221 GDP.15: 16 residues within 4Å: Chain J: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, V.174, D.176, E.180, N.203, Y.221, N.225 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:Q.10, J:C.11, J:N.98, J:S.137, J:G.141, J:T.142, J:T.142, J:G.143, J:E.180, J:N.203, J:N.225, J:N.225, J:N.225 pi-Stacking: J:Y.221, J:Y.221 GDP.18: 16 residues within 4Å: Chain L: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, V.174, D.176, E.180, N.203, Y.221, N.225 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:Q.10, L:C.11, L:N.98, L:S.137, L:G.141, L:T.142, L:T.142, L:G.143, L:E.180, L:N.203, L:N.225, L:N.225, L:N.225 pi-Stacking: L:Y.221, L:Y.221 GDP.21: 17 residues within 4Å: Chain C: L.247 Chain N: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, V.174, D.176, E.180, N.203, Y.221, N.225 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:Q.10, N:C.11, N:N.98, N:S.137, N:G.141, N:T.142, N:T.142, N:G.143, N:E.180, N:N.203, N:N.225, N:N.225, N:N.225 pi-Stacking: N:Y.221, N:Y.221 GDP.24: 17 residues within 4Å: Chain A: L.247 Chain P: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, V.174, D.176, E.180, N.203, Y.221, N.225 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:Q.10, P:C.11, P:N.98, P:S.137, P:G.141, P:T.142, P:T.142, P:G.143, P:E.180, P:N.203, P:N.225, P:N.225, P:N.225 pi-Stacking: P:Y.221, P:Y.221 GDP.27: 17 residues within 4Å: Chain E: L.247 Chain R: G.9, Q.10, C.11, Q.14, N.98, S.137, G.140, G.141, T.142, G.143, V.174, D.176, E.180, N.203, Y.221, N.225 15 PLIP interactions: 15 interactions with chain R Hydrogen bonds: R:Q.10, R:C.11, R:N.98, R:S.137, R:G.141, R:T.142, R:T.142, R:G.143, R:E.180, R:N.203, R:N.225, R:N.225, R:N.225 pi-Stacking: R:Y.221, R:Y.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shima, T. et al., Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport. J. Cell Biol. (2018)

Release Date

2018-10-10

Peptides

Tubulin alpha-1A chain: ACEGIKMOQ
Tubulin beta chain: BDFHJLNPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

Q
Q

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

Tubulin alpha-1A chain

Tubulin beta chain

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