SMTL ID : 4tuy.1

Tubulin-Rhizoxin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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 32 PLIP interactions: 27 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: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:E.71, A:E.71, A:N.101, A:F.141, A:T.145, A:A.174, A:T.179, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.7: 24 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.8 30 PLIP interactions: 25 interactions with chain C, 5 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:E.71, C:N.101, C:F.141, C:T.145, C:T.145, D:K.252, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: E.71 Chain D: K.252 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.10 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain F: E.331, N.333 Ligands: ACP.13 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.331, F:E.331

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:T.41, A:T.41, A:E.55, H2O.10 CA.9: 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:G.44, C:E.55, H2O.21

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

GDP.4: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, 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 Ligands: MG.5 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:V.175, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:E.69, B:S.138, B:G.140, B:G.140, B:T.143, B:S.145, B:S.145, B:D.177, B:D.177 pi-Stacking: B:Y.222, B:Y.222 GDP.10: 17 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.11 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:S.176, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:E.69, D:E.69, D:E.69, D:G.98, D:S.138, D:S.138, D:G.140, D:G.141, D:T.143, D:S.145, D:S.176, D:S.176

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

MES.6: 11 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, M.164, E.194, N.195, T.196, D.197, R.251 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:D.197, B:R.251 Water bridges: A:R.105

1 x 36L: (1R,2R,3E,5R,7R,8S,10S,13E,16R)-8-hydroxy-10-[(2S,3R,4E,6E,8E)-3-methoxy-4,8-dimethyl-9-(2-methyl-1,3-oxazol-4-yl)nona-4,6,8-trien-2-yl]-2,7-dimethyl-6,11,19-trioxatricyclo[14.3.1.0~5,7~]icosa-3,13-diene-12,18-dione(Non-covalent)

36L.12: 15 residues within 4Å: Chain D: G.98, N.99, N.100, K.103, D.177, T.178, V.179, V.180, A.387, M.388, R.391, A.393, F.394, W.397, Y.398 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.178, D:V.179, D:V.179, D:V.180, D:F.394, D:F.394, D:F.394, D:W.397, D:W.397, D:W.397, D:Y.398 Hydrogen bonds: D:N.100, D:V.179, D:V.180 Salt bridges: D:K.103

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

ACP.13: 19 residues within 4Å: Chain F: K.74, I.148, K.150, 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, E.331, N.333 Ligands: MG.14 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, 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:N.333, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prota, A.E. et al., A new tubulin-binding site and pharmacophore for microtubule-destabilizing anticancer drugs. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-08-27

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B 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-2B chain

Stathmin-4

Tubulin-Tyrosine Ligase

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