SMTL ID : 4zi7.1

CRYSTAL STRUCTURE OF TUBULIN-STATHMIN-TTL-HTI286 COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 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.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, I.231 Chain B: K.252 Ligands: MG.2 29 PLIP interactions: 24 interactions with chain A, 5 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: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:F.141, A:T.145, A:T.145, A:E.183, B:K.252, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.16: 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, P.173, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.17 27 PLIP interactions: 24 interactions with chain C, 3 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.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:F.141, C:T.145, C:T.145, C:E.183, 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)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: Q.11, E.69 Ligands: GDP.8 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain C: D.69, E.71 Chain D: K.252 Ligands: GTP.16 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Ligands: GDP.21 No protein-ligand interaction detected (PLIP)

4 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: 5 interactions with chain A Metal complexes: A:D.39, A:T.41, A:T.41, A:G.44, A:E.55 CA.10: 1 residues within 4Å: Chain B: E.111 No protein-ligand interaction detected (PLIP) CA.15: 1 residues within 4Å: Chain B: D.118 No protein-ligand interaction detected (PLIP) CA.18: 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:T.41, C:G.44, C:E.55, H2O.4

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: S.158, Y.161, G.162, K.164, K.166, E.196, D.199 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:K.164, A:K.166, E:D.42 GOL.5: 7 residues within 4Å: Chain A: N.216, A.273, P.274, V.275, I.276, A.294, N.300 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.216, A:V.275, A:V.275, A:N.300 Water bridges: A:N.216, A:N.216 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:R.221, A:Y.224 GOL.7: 6 residues within 4Å: Chain A: R.105, T.109, G.410, E.411 Chain E: R.59 Ligands: MES.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.105 GOL.13: 5 residues within 4Å: Chain B: R.390, R.391 Chain C: Y.262, E.434 Ligands: GOL.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.262 GOL.19: 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.20: 5 residues within 4Å: Chain C: Y.262, R.264, D.431, V.435 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.431, C:D.431 GOL.24: 6 residues within 4Å: Chain F: Y.211, R.292, M.296, L.378, H.379, H.380 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.211, F:R.292, F:H.380, F:H.380

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

GDP.8: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.9 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.141, 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:S.138, B:G.140, B:T.143, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.21: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.22 20 PLIP interactions: 20 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: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:N.99, D:S.138, D:S.145 pi-Stacking: D:Y.222, D:Y.222

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

MES.11: 12 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, T.196, D.197, R.251 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.197, B:R.251 MES.12: 9 residues within 4Å: Chain B: F.294, D.295, A.296, D.304, P.305, R.306, V.333, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.296, B:R.306 Salt bridges: B:R.306

1 x 4SL: N,beta,beta-trimethyl-L-phenylalanyl-N-[(3S,4Z)-5-carboxy-2-methylhex-4-en-3-yl]-N,3-dimethyl-L-valinamide(Non-covalent)

4SL.14: 13 residues within 4Å: Chain B: P.173, K.174, V.175, D.177, P.220, T.221, Y.222 Chain C: L.248, P.325, N.329, I.332, F.351, V.353 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.248, C:P.325, C:V.353, B:Y.222 Hydrogen bonds: C:N.329, C:N.329, B:D.177, B:P.220

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

ACP.23: 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 15 PLIP interactions: 15 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:D.318, F:D.318, F:E.331, F:N.333 Salt bridges: F:K.74

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

2016-07-27

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD
Stathmin-4: E
Tubulin-Tyrosine Ligase: 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

Tubulin-Tyrosine Ligase

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