SMTL ID : 3e22.1

Tubulin-colchicine-soblidotin: Stathmin-like domain complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 26 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228 Chain B: K.252 Ligands: MG.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.10, A:Q.11, A:A.12, A:E.71, A:D.98, A:S.140, A:G.144, A:T.145, A:G.146, A:S.178, A:E.183, A:N.206, A:Y.224, A:N.228, A:N.228, A:N.228 pi-Stacking: A:Y.224 Salt bridges: B:K.252 GTP.6: 25 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, E.183, N.206, Y.224, L.227, N.228 Chain D: K.252 Ligands: MG.7 19 PLIP interactions: 2 interactions with chain D, 17 interactions with chain C Salt bridges: D:K.252, D:K.252 Hydrogen bonds: C:G.10, C:Q.11, C:A.12, C:E.71, C:D.98, C:S.140, C:G.144, C:T.145, C:G.146, C:S.178, C:E.183, C:N.206, C:Y.224, C:N.228, C:N.228, C:N.228 pi-Stacking: C:Y.224

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.98, A.99, N.101, G.144, T.145 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain C: D.98, N.101, G.144, T.145 Chain D: K.252 Ligands: GTP.6 No protein-ligand interaction detected (PLIP)

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

GDP.3: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:N.99, B:S.138, B:G.142, B:T.143, B:G.144, B:S.145, B:V.175, B:S.176, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 GDP.8: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, N.99, S.138, G.140, G.141, G.142, T.143, G.144, P.171, V.175, S.176, D.177, E.181, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:N.99, D:S.138, D:G.142, D:T.143, D:G.144, D:V.175, D:D.177, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226

2 x LOC: N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide(Non-covalent)

LOC.4: 20 residues within 4Å: Chain A: S.178, T.179, A.180, V.181 Chain B: V.236, T.237, C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, V.316, N.348, V.349, K.350 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.246, B:A.248, B:K.252, B:L.253, B:K.350 Hydrogen bonds: B:L.240, B:N.256, A:V.181 LOC.9: 20 residues within 4Å: Chain C: S.178, T.179, A.180, V.181 Chain D: V.236, T.237, C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, V.316, N.348, V.349, K.350 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.246, D:A.248, D:K.252, D:L.253, D:K.350, C:A.180 Hydrogen bonds: D:N.256, C:V.181

1 x TZT: SOBLIDOTIN(Non-covalent)

TZT.5: 16 residues within 4Å: Chain B: Q.11, Q.15, T.72, S.75, V.175, S.176, D.177, P.220, T.221, Y.222, G.223 Chain C: L.248, P.325, V.328, N.329, F.351 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Q.11, B:T.72, B:Y.222, B:Y.222, C:P.325, C:V.328 Hydrogen bonds: B:Y.222, B:G.223, B:N.226 Salt bridges: B:D.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cormier, A. et al., Structural insight into the inhibition of tubulin by vinca domain peptide ligands. Embo Rep. (2008)

Release Date

2008-10-21

Peptides

Tubulin alpha-1C chain: AC
Tubulin beta-2B chain: BD
Stathmin-4: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

Tubulin alpha-1C chain

Tubulin beta-2B chain

Stathmin-4

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