SMTL ID : 4eb6.1

Tubulin-Vinblastine: Stathmin-like complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.47 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, I.171, P.173, V.177, S.178, E.183, N.206, Y.224, N.228 Chain B: K.252 Ligands: MG.2 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:Q.11, A:A.12, A:A.99, A:N.101, A:S.140, A:G.144, A:T.145, A:V.177, A:E.183, A:N.206, A:N.228, A:N.228, A:N.228 Water bridges: A:E.71, A:D.98, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.7: 26 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, 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 Chain D: K.252 Ligands: MG.8 23 PLIP interactions: 19 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:Q.11, C:A.12, C:A.99, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:S.178, C:E.183, C:N.206, C:N.228, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Water bridges: D:K.252, D:K.252, D:K.252 Salt bridges: D:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: Q.11 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain C: Q.11 Ligands: GTP.7 No protein-ligand interaction detected (PLIP)

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.347 Salt bridges: A:K.394 SO4.4: 5 residues within 4Å: Chain A: V.177, S.178, R.221, P.222, Y.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.178, A:S.178 Salt bridges: A:R.221 SO4.6: 4 residues within 4Å: Chain B: T.221, G.223, D.224, R.276 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.221, B:G.223, B:D.224 Salt bridges: B:R.276 SO4.11: 6 residues within 4Å: Chain D: K.19, E.22, V.23, G.223, H.227, R.276 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.22, D:E.22, D:S.230 Salt bridges: D:K.19, D:H.227 SO4.12: 3 residues within 4Å: Chain D: T.221, G.223, R.276 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.223 Salt bridges: D:R.276

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

GDP.5: 21 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, D.67, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:D.67, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:G.144, B:S.176, B:S.176, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 Water bridges: B:G.13, B:S.138, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.10: 20 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, V.169, P.171, V.175, D.177, E.181, N.204, L.207, Y.222, N.226 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:V.175, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:S.145 pi-Stacking: D:Y.222, D:Y.222

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

VLB.9: 17 residues within 4Å: Chain B: P.173, K.174, V.175, D.177, Y.208, T.218, T.219, P.220, T.221, Y.222 Chain C: P.325, N.329, I.332, K.336, F.351, V.353, I.355 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:Y.222, B:Y.222, C:P.325, C:P.325, C:V.353, C:V.353, C:I.355 Hydrogen bonds: B:T.221, C:N.329, C:N.329 Salt bridges: B:D.177, C:K.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ranaivoson, F.M. et al., Structural plasticity of tubulin assembly probed by vinca-domain ligands. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-08-01

Peptides

Tubulin alpha chain: AC
Tubulin beta 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 chain

Tubulin beta chain

Stathmin-4

Related Entries With Identical Sequence