SMTL ID : 4i55.1

Crystal structure of tubulin-stathmin-TTL complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 32 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: Q.245, K.252 Ligands: MG.2 27 PLIP interactions: 21 interactions with chain A, 6 interactions with chain B Hydrogen bonds: 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:T.145, A:G.146, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:F.141, A:T.179, A:E.183, B:Q.245, 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.12: 32 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, L.70, D.98, A.99, A.100, N.101, N.102, 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.13 29 PLIP interactions: 24 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:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:N.101, C:S.140, C:F.141, C:V.177, C:T.179, C:T.179, 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, D:K.252

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 6 residues within 4Å: Chain A: Q.11, D.69, E.71, D.98 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.6 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain B: D.114 No protein-ligand interaction detected (PLIP) MG.13: 6 residues within 4Å: Chain C: Q.11, D.69, E.71, D.98 Chain D: K.252 Ligands: GTP.12 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain D: Q.11, N.99, D.177 Ligands: GDP.15 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.177, H2O.26 MG.17: 6 residues within 4Å: Chain F: R.222, N.242, D.318, I.330, E.331 Ligands: ACP.19 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.318 MG.18: 5 residues within 4Å: Chain A: E.450 Chain F: K.74, E.331, N.333 Ligands: ACP.19 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, F.49, E.55, H.61 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:D.39, A:G.44, A:E.55, H2O.3 CA.5: 3 residues within 4Å: Chain A: K.166, H.197 Chain E: D.42 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain B: E.111 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.111, H2O.9, H2O.10, H2O.10 CA.14: 7 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, F.49, E.55, H.61 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.19

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

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

GDP.6: 27 residues within 4Å: Chain B: G.10, Q.11, C.12, 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.7 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:D.67, B:E.69, B:S.138, B:G.140, B:G.140, B:T.143, B:S.145, B:S.145, B:D.177 pi-Stacking: B:Y.222, B:Y.222 GDP.15: 29 residues within 4Å: Chain D: G.10, Q.11, C.12, G.13, 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.16 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:Q.15, 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:S.138, D:G.141, D:T.143, D:S.145

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

MES.9: 12 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 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:R.105, A:R.105, B:R.156 Salt bridges: B:D.197, B:R.251 MES.10: 12 residues within 4Å: Chain B: F.294, D.295, S.296, K.297, M.299, P.305, R.306, Y.310, V.333, N.337, Y.340, F.341 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.294, B:D.295, B:S.296 Water bridges: B:S.296, B:S.296 Salt bridges: B:R.306

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

ACP.19: 24 residues within 4Å: Chain A: E.450 Chain F: K.74, P.95, 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, M.320, I.330, E.331, N.333 Ligands: MG.17, MG.18 21 PLIP interactions: 18 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:K.74, F:K.150, F:K.184, F:L.186, F:K.198, F:D.200, F:D.200, F:R.202, F:R.222, F:T.241, F:T.241, F:N.242, F:N.242, F:E.331, F:N.333, F:N.333, A:E.450, A:E.450, A:E.450 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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