SMTL ID : 1z2b.1

Tubulin-colchicine-vinblastine: stathmin-like domain complex

Coordinates

PDB Format

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.2 No protein-ligand interaction detected (PLIP) MG.5: 7 residues within 4Å: Chain C: D.98, A.99, N.101, G.144, T.145 Chain D: K.252 Ligands: GTP.6 No protein-ligand interaction detected (PLIP)

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

GTP.2: 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, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.1 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.10, A:Q.11, A:Q.11, A:A.12, A:D.98, A:A.99, 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, A:Y.224 Salt bridges: B:K.252 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, I.231 Chain D: K.252 Ligands: MG.5 17 PLIP interactions: 16 interactions with chain C, 1 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, C:Y.224 Salt bridges: D:K.252

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

GDP.3: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, P.171, S.176, E.181, N.204, Y.222, N.226 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:Q.11, B:C.12, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:S.145, B:S.176, B:S.176, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.8: 19 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, N.99, S.138, G.140, G.141, G.142, T.143, G.144, P.171, V.175, D.177, E.181, N.204, Y.222, L.225, N.226 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:N.99, D:S.138, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:S.145, D:V.175, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226

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)

CN2.4: 19 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, N.348, V.349, K.350, I.368 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.248, B:K.252, B:L.253, B:L.253, B:N.256 Hydrogen bonds: A:S.178, A:V.181 CN2.9: 18 residues within 4Å: Chain C: S.178, T.179, A.180, V.181 Chain D: V.236, C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, N.348, K.350, I.368 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.246, D:A.248, D:K.252, D:L.253, D:L.253 Hydrogen bonds: C:S.178, C:V.181

1 x VLB: (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE(Non-covalent)

VLB.7: 18 residues within 4Å: Chain B: P.173, K.174, V.175, D.177, Y.208, F.212, T.218, T.219, P.220, T.221, Y.222, L.225 Chain C: P.325, V.328, N.329, F.351, V.353, I.355 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:P.325, C:P.325, C:V.328, C:V.328, C:N.329, C:V.353, C:I.355, B:V.175, B:Y.208, B:Y.222, B:L.225 Hydrogen bonds: C:N.329 Salt bridges: B:D.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gigant, B. et al., Structural basis for the regulation of tubulin by vinblastine. Nature (2005)

Release Date

2005-05-31

Peptides

Tubulin alpha chain: AC
Tubulin beta chain: BD
RB3 STATHMIN-LIKE DOMAIN 4: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

Tubulin alpha chain

Tubulin beta chain

RB3 STATHMIN-LIKE DOMAIN 4

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