SMTL ID : 3ut5.1

Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

hetero-2-2-1-mer

Ligands

1 x 0EA- VAL- 0E5- GLY: Vinca tetrapeptide(Non-covalent)

0EA-VAL-0E5-GLY.1: 17 residues within 4Å: Chain B: K.174, V.175, D.177, Y.208, T.219, P.220, T.221, Y.222 Chain C: L.248, P.325, V.328, N.329, I.332, F.351, V.353, I.355 Ligands: SO4.8 14 PLIP interactions: 7 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:L.248, C:P.325, C:V.328, C:V.353, C:I.355, B:Y.222, B:Y.222, B:Y.222 Hydrogen bonds: C:N.329, C:N.329, B:K.174, B:P.220, B:Y.222 pi-Stacking: B:Y.208

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

GTP.2: 25 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, G.146, I.171, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.3 27 PLIP interactions: 22 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:F.141, A:T.145, A:T.145, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.9: 25 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, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.10 28 PLIP interactions: 23 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:A.99, C:A.100, C:N.101, 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:N.228, C:N.228 Water bridges: C:G.13, C:E.71, C:S.140, C:T.145, C:T.145, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: N.247 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain D: N.247 Ligands: GTP.9 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.394 Hydrogen bonds: B:N.347 SO4.5: 5 residues within 4Å: Chain A: V.177, S.178, R.221, P.222, Y.224 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.245, A:Q.176, A:S.178 Salt bridges: A:R.221 SO4.8: 4 residues within 4Å: Chain B: T.221, G.223, R.276 Ligands: 0EA-VAL-0E5-GLY.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.223 Salt bridges: B:R.276 SO4.13: 4 residues within 4Å: Chain D: K.19, H.227, R.276, G.277 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.277 Salt bridges: D:K.19, D:H.227 SO4.14: 2 residues within 4Å: Chain D: T.221, R.276 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.221 Salt bridges: D:R.276

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

GDP.6: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, 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:Q.11, B:C.12, B:Q.15, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 Water bridges: B:S.138, B:L.139, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.11: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:Q.15, 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.226, D:N.226, D:N.226 Water bridges: D:G.13, D:N.99, D:S.145 pi-Stacking: D:Y.222, D:Y.222

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.7: 18 residues within 4Å: Chain A: T.179, A.180, V.181 Chain B: C.239, L.240, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.348, K.350, I.368 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.248, B:K.252, B:L.253, B:L.253, B:N.256, B:A.314, B:K.350, B:K.350 Hydrogen bonds: A:V.181 LOC.12: 18 residues within 4Å: Chain C: T.179, A.180, V.181 Chain D: C.239, L.240, Q.245, A.248, D.249, K.252, L.253, N.256, M.257, V.313, A.314, N.348, K.350, A.352, I.368 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.248, D:K.252, D:L.253, D:L.253, D:N.256, D:A.314, D:K.350, D:K.350 Hydrogen bonds: D:Q.245, C:V.181 Water bridges: D:L.240

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

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