SMTL ID : 3du7.1

Tubulin-colchicine-phomopsin A: Stathmin-like domain complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.10 Å

Oligo State

hetero-2-2-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.98, A.99, N.101, G.144, T.145 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.4: 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 CN2: 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE(Non-covalent)

CN2.2: 17 residues within 4Å: Chain A: S.178, T.179, A.180, V.181 Chain B: V.236, C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, V.316, K.350 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.248, B:L.253 CN2.9: 18 residues within 4Å: Chain C: S.178, T.179, A.180, V.181 Chain D: V.236, C.239, L.240, A.248, K.252, L.253, N.256, M.257, V.313, A.314, V.316, N.348, K.350, I.368 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.248, D:K.252, D:L.253, D:N.256 Hydrogen bonds: C:V.181

2 x HOS: Phomopsin A(Non-covalent)

HOS.3: 15 residues within 4Å: Chain B: P.173, V.175, S.176, D.177, T.219, P.220, T.221, Y.222, G.223 Chain C: P.325, V.328, N.329, F.351, V.353, I.355 17 PLIP interactions: 5 interactions with chain C, 12 interactions with chain B Hydrophobic interactions: C:P.325, C:V.328, C:V.353, C:I.355, B:V.175, B:V.175, B:Y.222, B:Y.222, B:Y.222 Hydrogen bonds: C:N.329, B:P.173, B:V.175, B:S.176, B:D.177, B:T.221, B:Y.222, B:G.223 HOS.10: 9 residues within 4Å: Chain D: V.175, S.176, D.177, Y.208, T.219, P.220, T.221, Y.222, G.223 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.175, D:T.219, D:T.221, D:Y.222, D:Y.222, D:Y.222 Hydrogen bonds: D:V.175, D:S.176, D:T.221, D:Y.222, D:G.223

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

GTP.5: 26 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, 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, N.228, M.231 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.11, A:A.12, A:D.98, A:S.140, A:T.145, A:G.146, A:S.178, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 GTP.6: 26 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, 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, N.228, M.231 Chain D: K.252 Ligands: MG.4 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, 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:N.206, C:Y.224, C:N.228, C:N.228 pi-Stacking: C:Y.224 Salt bridges: D:K.252, D:K.252

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

GDP.7: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, S.138, G.140, G.142, T.143, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:Q.11, B:C.12, B:D.67, B:S.138, B:G.142, B:T.143, B:V.175, B:E.181, B:N.204, B:N.204, B:N.226 GDP.8: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, I.16, D.67, N.99, S.138, G.140, G.142, T.143, P.171, V.175, S.176, E.181, N.204, L.207, Y.222, N.226 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:S.176, D:S.176, D:E.181, D:E.181, D:N.204, D:N.204, D:N.226

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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