SMTL ID : 7ysq.1

GTPgammaS Tube decorated with kinesin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

GTP.1: 19 residues within 4Å: Chain A: Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, I.171, T.179, N.206, Y.224, L.227, N.228 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:Q.11, A:Q.11, A:D.69, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:T.179, A:T.179, A:N.206, A:N.206 pi-Cation interactions: A:Y.224 Salt bridges: F:K.252, F:K.252 GTP.3: 22 residues within 4Å: Chain C: Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, I.171, T.179, N.206, Y.224, L.227, N.228 Chain H: Q.245, L.246, K.252 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain H Hydrogen bonds: C:Q.11, C:Q.11, C:D.69, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:T.179, C:T.179, C:N.206, C:N.206 pi-Cation interactions: C:Y.224 Salt bridges: H:K.252, H:K.252, H:K.252 GTP.4: 21 residues within 4Å: Chain B: L.246, K.252 Chain D: Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, I.171, T.179, N.206, Y.224, L.227, N.228 19 PLIP interactions: 3 interactions with chain B, 16 interactions with chain D Salt bridges: B:K.252, B:K.252, B:K.252 Hydrogen bonds: D:Q.11, D:Q.11, D:D.69, D:A.99, D:A.100, D:N.101, D:N.101, D:S.140, D:G.144, D:T.145, D:T.145, D:T.179, D:T.179, D:N.206, D:N.206 pi-Cation interactions: D:Y.224 GTP.5: 19 residues within 4Å: Chain E: Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, I.171, T.179, N.206, Y.224, L.227, N.228 18 PLIP interactions: 16 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:Q.11, E:Q.11, E:D.69, E:A.99, E:A.100, E:N.101, E:N.101, E:S.140, E:G.144, E:T.145, E:T.145, E:T.179, E:T.179, E:N.206, E:N.206 pi-Cation interactions: E:Y.224 Salt bridges: G:K.252, G:K.252

4 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.2: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, G.98, N.99, S.138, G.141, G.142, T.143, D.177, Y.208, Y.222, L.225, N.226 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:Q.11, B:Q.11, B:C.12, B:Q.15, B:G.98, B:N.99, B:N.99, B:S.138, B:G.141, B:G.142, B:T.143, B:N.204, B:Y.208, B:Y.222, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 pi-Cation interactions: B:Y.222 GSP.6: 15 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, G.98, N.99, S.138, G.141, G.142, T.143, D.177, Y.208, Y.222, L.225, N.226 21 PLIP interactions: 21 interactions with chain F Hydrogen bonds: F:Q.11, F:Q.11, F:Q.11, F:Q.11, F:C.12, F:Q.15, F:G.98, F:N.99, F:N.99, F:S.138, F:G.141, F:G.142, F:T.143, F:N.204, F:Y.208, F:Y.222, F:N.226, F:N.226 pi-Stacking: F:Y.222, F:Y.222 pi-Cation interactions: F:Y.222 GSP.7: 15 residues within 4Å: Chain G: G.10, Q.11, C.12, Q.15, G.98, N.99, S.138, G.141, G.142, T.143, D.177, Y.208, Y.222, L.225, N.226 21 PLIP interactions: 21 interactions with chain G Hydrogen bonds: G:Q.11, G:Q.11, G:Q.11, G:Q.11, G:C.12, G:Q.15, G:G.98, G:N.99, G:N.99, G:S.138, G:G.141, G:G.142, G:T.143, G:N.204, G:Y.208, G:Y.222, G:N.226, G:N.226 pi-Stacking: G:Y.222, G:Y.222 pi-Cation interactions: G:Y.222 GSP.8: 15 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, G.98, N.99, S.138, G.141, G.142, T.143, D.177, Y.208, Y.222, L.225, N.226 21 PLIP interactions: 21 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:Q.11, H:Q.11, H:C.12, H:Q.15, H:G.98, H:N.99, H:N.99, H:S.138, H:G.141, H:G.142, H:T.143, H:N.204, H:Y.208, H:Y.222, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222 pi-Cation interactions: H:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun (2023)

Release Date

2023-10-18

Peptides

Tubulin alpha chain: ACDE
Tubulin beta-1 chain: BFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

D
E

E
F

B
B

F
G

G
H

H
I

Tubulin alpha chain

Tubulin beta-1 chain

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