SMTL ID : 4i4t.1

Crystal structure of tubulin-RB3-TTL-Zampanolide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 31 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, L.70, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 30 PLIP interactions: 25 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:T.145, A:G.146, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:L.70, A:N.101, A:N.101, A:S.140, A:F.141, A:A.174, A:A.174, 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.16: 30 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.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.17 27 PLIP interactions: 21 interactions with chain C, 6 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:G.144, C:T.145, C:G.146, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:S.140, C:F.141, C:T.179, C:T.179, C:E.183, 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, D:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Q.11, E.71, D.98 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.9 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain C: Q.11, E.71, D.98 Chain D: K.252 Ligands: GTP.16 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain D: Q.11, N.99, D.177 Ligands: GDP.19 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain F: D.318, I.330, E.331 Ligands: ACP.24 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain A: E.450 Chain F: K.74, E.331, N.333 Ligands: ACP.24 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.331, F:E.331, H2O.51, H2O.56, H2O.57

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 6 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, F.49, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:G.44, A:E.55, A:E.55, H2O.4 CA.5: 1 residues within 4Å: Ligands: GOL.7 No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Chain B: E.108, E.111 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.111, H2O.16, H2O.18, H2O.18, H2O.22 CA.18: 7 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, F.49, E.55, H.61 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.39, C:T.41, C:G.44, C:E.55, C:E.55

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: Y.161, G.162, K.163, K.164 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: R.105, T.109, G.410, E.411 Chain B: D.161, R.251 Chain E: R.59 Ligands: MES.15 9 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B, 1 interactions with chain E Hydrogen bonds: A:R.105, B:D.161, B:R.251, B:R.251 Water bridges: B:D.161, B:D.161, B:D.161, B:D.161, E:E.63 GOL.7: 7 residues within 4Å: Chain A: G.162, K.163, K.164, S.165, D.199, T.253 Ligands: CA.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.162, A:S.165, A:S.165, A:D.199 Water bridges: A:K.166, A:K.166 GOL.8: 8 residues within 4Å: Chain A: N.216, A.273, P.274, V.275, I.276, L.286, A.294, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.275 Water bridges: A:N.216, A:N.300 GOL.12: 8 residues within 4Å: Chain B: Q.291, F.294, D.295, S.296, K.297, P.305, R.306 Ligands: GOL.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.294, B:D.295, B:S.296, B:S.296 Water bridges: B:F.294, B:S.296 GOL.13: 9 residues within 4Å: Chain B: F.294, P.305, R.306, Y.310, V.333, N.337, Y.340, F.341 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.306 GOL.25: 10 residues within 4Å: Chain F: Y.211, N.212, I.213, R.292, M.296, E.299, L.378, H.379, H.380, H.381 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.292, F:H.380, F:H.380, F:H.381 Water bridges: F:I.213, F:L.378 GOL.26: 8 residues within 4Å: Chain F: K.288, H.289, R.292, I.376, K.377, L.378, H.379, H.380 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:K.288, F:R.292, F:R.292, F:K.377, F:H.379 Water bridges: F:H.289

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

GDP.9: 28 residues within 4Å: Chain B: G.10, Q.11, C.12, G.13, Q.15, I.16, A.97, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.10 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:Q.15, 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.141, B:T.143, B:S.145, B:D.177 pi-Stacking: B:Y.222, B:Y.222 GDP.19: 28 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.20 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:Q.15, D:N.99, D:S.138, 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:G.13, D:D.67, D:G.140, D:G.141, D:T.143, D:S.145 pi-Stacking: D:Y.222, D:Y.222

1 x TYR: TYROSINE(Non-covalent)

TYR.14: 7 residues within 4Å: Chain B: R.391 Chain C: Y.262, R.264, I.265, D.431, E.434, V.435 10 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: C:D.431, C:E.434, C:V.435 Water bridges: C:E.434, Y.14, Y.14 pi-Stacking: C:Y.262 Hydrogen bonds: B:R.391, B:R.391 Salt bridges: B:R.391

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

MES.15: 13 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, E.194, N.195, T.196, D.197, R.251 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.156, B:R.156 Water bridges: B:R.251 Salt bridges: B:D.197, B:R.251

1 x ZPN: (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide(Covalent)

ZPN.21: 20 residues within 4Å: Chain D: V.23, L.215, H.227, L.228, A.231, S.234, F.270, P.272, L.273, T.274, R.276, Q.279, R.282, A.283, L.284, E.288, Q.292, P.358, R.359, L.361 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:A.231, D:F.270, D:P.272, D:P.272, D:Q.279, D:R.282, D:L.284, D:P.358, D:L.361, D:L.361 Hydrogen bonds: D:T.274, D:Q.279 Water bridges: D:H.227, D:R.276, D:Q.279 Salt bridges: D:H.227

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

ACP.24: 25 residues within 4Å: Chain A: E.450 Chain F: K.74, P.95, I.148, K.150, I.160, 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, M.320, I.330, E.331, N.333 Ligands: MG.22, MG.23 21 PLIP interactions: 20 interactions with chain F, 1 interactions with chain A 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:T.241, F:T.241, F:N.242, F:D.318, F:E.331, F:E.331, F:N.333, A:E.450 Water bridges: F:G.154, F:K.156, F:E.331 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prota, A.E. et al., Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science (2013)

Release Date

2013-01-23

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B chain: BD
Stathmin-4: E
Tubulin Tyrosine ligase, TTL: 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, TTL

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