SMTL ID : 7cld.1

Crystal structure of T2R-TTL-Cevipabulin complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

3 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, 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 29 PLIP interactions: 4 interactions with chain B, 25 interactions with chain A Water bridges: B:K.252, B:K.252, B:K.252, A:G.13, A:F.141, A:A.174 Salt bridges: B:K.252 Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:T.145, A:G.146, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 GTP.11: 27 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, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.12, G2X.14 31 PLIP interactions: 24 interactions with chain C, 7 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:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:N.206, C:N.206, C:Y.224, C:Y.224, C:N.228, C:N.228 Water bridges: C:G.13, C:E.71, C:T.179, 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, D:K.252 GTP.18: 29 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, D.67, A.97, G.98, N.99, N.100, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, S.172, V.175, S.176, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.16 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:Q.15, D:A.97, D:G.98, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:S.176, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:G.13 pi-Stacking: D:Y.222, D:Y.222

5 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.6: 3 residues within 4Å: Chain B: Q.11, E.69 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain C: Q.11, E.71, D.98 Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain D: Q.11, D.67 Ligands: GTP.18 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.20 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

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

CA.3: 7 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, F.49, N.50, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:D.39, A:T.41, A:G.44, A:E.55 CA.4: 2 residues within 4Å: Chain A: S.158, G.162 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain B: D.114 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain B: E.108, E.111 No protein-ligand interaction detected (PLIP) CA.13: 7 residues within 4Å: Chain C: D.39, T.41, I.42, G.43, E.55, G.59, H.61 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.55 CA.15: 6 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, F.49, 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.6 CA.17: 1 residues within 4Å: Chain D: V.175 No protein-ligand interaction detected (PLIP)

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

GDP.5: 21 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, D.177, N.204, L.207, Y.222, L.225, N.226 Ligands: MG.6 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 Water bridges: B:A.97, B:N.99, B:N.99, B:N.99, B:S.138, B:G.141, B:T.143, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222

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

MES.7: 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 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.156 Salt bridges: B:D.197, B:R.251

2 x G2X: 6-[2,6-bis(fluoranyl)-4-[3-(methylamino)propoxy]phenyl]-5-chloranyl-N-[(2S)-1,1,1-tris(fluoranyl)propan-2-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine(Non-covalent)

G2X.10: 20 residues within 4Å: Chain B: K.174, V.175, D.177, N.204, E.205, Y.208, D.209, R.213, P.220, T.221, Y.222, L.225 Chain C: A.247, L.248, P.325, K.326, V.328, N.329, V.353, I.355 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:N.329, B:D.177, B:Y.208, B:Y.208, B:Y.208 Halogen bonds: C:P.325, C:N.329 Hydrogen bonds: B:Y.222 pi-Stacking: B:Y.222, B:Y.222 G2X.14: 15 residues within 4Å: Chain C: V.177, S.178, T.179, N.206, E.207, Y.210, D.211, R.214, R.221, P.222, T.223, Y.224, L.227 Chain D: Q.245 Ligands: GTP.11 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.206, C:E.207, C:Y.210 Hydrogen bonds: C:Y.224, C:Y.224 Water bridges: C:E.207, C:E.207 pi-Stacking: C:Y.224, C:Y.224 Halogen bonds: C:N.206, C:R.221

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

ACP.20: 23 residues within 4Å: 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.19 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, F:Q.183, F:K.184, F:L.186, F:K.198, F:D.200, F:R.202, F:R.222, F:H.239, F:T.241, F:T.241, F:D.318, F:E.331, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Cevipabulin-tubulin complex reveals a novel agent binding site on alpha-tubulin with tubulin degradation effect. Sci Adv (2021)

Release Date

2021-07-07

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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