SMTL ID : 5bmv.1

CRYSTAL STRUCTURE OF TUBULIN-STATHMIN-TTL-Vinblastine COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 25 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 29 PLIP interactions: 26 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:A.99, A:N.101, A:S.140, A:G.144, A:T.145, 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:E.71, A:E.71, A:F.141, A:T.145, A:T.145, A:E.183, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.13: 25 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.14 31 PLIP interactions: 27 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, C:A.99, C:A.100, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:G.13, C:E.71, C:E.71, C:F.141, C:T.145, C:T.145, C:E.183, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.7 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain D: A.97, T.143 Ligands: GDP.20 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:D.39, A:T.41, A:G.44, H2O.1 CA.9: 1 residues within 4Å: Chain B: E.111 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.111, H2O.4 CA.15: 4 residues within 4Å: Chain C: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:D.39, C:T.41, C:G.44, H2O.6

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: S.158, G.162, K.164, K.166, E.196, H.197, D.199 Chain E: D.42 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:D.42, A:S.158, A:K.166, A:D.199 GOL.5: 6 residues within 4Å: Chain A: N.216, P.274, V.275, I.276, A.294, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.216, A:V.275, A:N.300 GOL.6: 4 residues within 4Å: Chain A: V.177, R.221, T.223, Y.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.177, A:Y.224 GOL.12: 4 residues within 4Å: Chain B: R.391 Chain C: Y.262, E.434 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.262, C:E.434, C:E.434 GOL.16: 5 residues within 4Å: Chain C: Y.172, D.205, E.207, K.304, R.390 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.205, C:E.207, C:R.390 GOL.17: 6 residues within 4Å: Chain C: A.19, E.22, L.23, R.229, S.232, V.363 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.22, C:R.229, C:S.232, C:Q.233 Water bridges: C:E.22 GOL.18: 4 residues within 4Å: Chain C: D.431, E.434, V.435 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.431, C:E.434, C:E.434

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

GDP.7: 19 residues within 4Å: Chain B: 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, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.8 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:Q.11, B:G.13, B:E.69, B:G.98, B:G.140, B:G.141, B:T.143, B:S.145, B:S.176, B:S.176 pi-Stacking: B:Y.222, B:Y.222 GDP.20: 20 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.21 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:G.13, D:S.138 pi-Stacking: D:Y.222, D:Y.222

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.10: 9 residues within 4Å: Chain B: R.156, P.160, D.161, R.162, M.164, N.195, T.196, D.197, R.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.156 Salt bridges: B:D.197, B:R.251 MES.11: 8 residues within 4Å: Chain B: F.294, D.295, A.296, D.304, R.306, V.333, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.295, B:A.296 Salt bridges: B:R.306

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

VLB.19: 22 residues within 4Å: Chain B: P.173, K.174, V.175, S.176, D.177, Y.208, F.212, T.218, T.219, P.220, T.221, Y.222, L.225 Chain C: P.325, K.326, V.328, N.329, I.332, A.333, F.351, V.353, I.355 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:P.325, C:P.325, C:V.328, C:N.329, C:I.332, C:F.351, C:V.353, C:I.355, B:Y.208, B:Y.222, B:L.225 Hydrogen bonds: C:N.329, C:N.329 Salt bridges: C:K.336, C:K.336, B:D.177

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.22: 18 residues within 4Å: Chain F: K.74, I.148, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, H.239, L.240, T.241, N.242, D.318, I.330, E.331, N.333 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:K.74, F:Q.183, F:L.186, F:K.198, F:D.200, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:N.242, F:D.318, F:N.333, F:N.333 Salt bridges: F:K.74 pi-Stacking: F:Y.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structural Insights into the Pharmacophore of Vinca Domain Inhibitors of Microtubules. Mol.Pharmacol. (2016)

Release Date

2016-07-13

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD
Stathmin-4: E
Uncharacterized protein: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Tubulin alpha-1B chain

Tubulin beta chain

Stathmin-4

Uncharacterized protein

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