SMTL ID : 6knz.1

Crystal structure of T2R-TTL-KXO1 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

3 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, 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, A.180, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2, DN0.9 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:D.98, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:T.179, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:S.140, A:F.141, A:G.142, A:T.145, A:T.145, B:N.247, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.11: 32 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, A.180, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.12, DN0.17 28 PLIP interactions: 24 interactions with chain C, 4 interactions with chain D Hydrogen bonds: 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:G.146, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:Q.11, C:G.13, C:G.142, C:G.142, C:T.145, C:T.145, C:V.177, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252 GTP.16: 30 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, D.67, E.69, A.97, G.98, 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, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.14 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:Q.11, D:C.12, D:A.97, D:N.99, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:G.144, D:S.176, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

5 x MG: MAGNESIUM ION(Non-covalent)

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.5: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.12: 6 residues within 4Å: Chain C: Q.11, D.69, E.71, D.98 Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain D: Q.11, E.69 Ligands: GTP.16 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

6 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:T.41, A:G.44, A:E.55, H2O.1 CA.7: 1 residues within 4Å: Chain B: D.114 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain B: E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.13: 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.4 CA.15: 4 residues within 4Å: Chain D: V.175, P.220, T.221, Y.222 No protein-ligand interaction detected (PLIP) CA.18: 4 residues within 4Å: Chain A: S.158, K.166, H.197 Chain E: D.42 No protein-ligand interaction detected (PLIP)

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

GDP.4: 28 residues within 4Å: Chain B: 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.5 22 PLIP interactions: 22 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:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:G.98, B:S.138, B:G.140, B:G.140, B:G.141, B:T.143, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222

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

MES.6: 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 MES.10: 12 residues within 4Å: Chain B: F.294, D.295, S.296, K.297, D.304, P.305, R.306, Y.310, V.333, N.337, Y.340, F.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.296 Salt bridges: B:R.306

2 x DN0: 2-[5-[4-(2-morpholin-4-ylethoxy)phenyl]pyridin-2-yl]-~{N}-(phenylmethyl)ethanamide(Non-covalent)

DN0.9: 32 residues within 4Å: Chain A: N.101, S.178, T.179, A.180, E.183, Y.224 Chain B: I.4, Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, C.239, L.240, L.246, N.247, A.248, L.250, K.252, L.253, N.256, M.257, A.314, I.316, K.350, T.351, A.352, I.368 Ligands: GTP.1 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.165, B:F.167, B:F.167, B:Y.200, B:V.236, B:T.237, B:L.240, B:L.246, B:L.250, B:L.253, B:L.253, B:A.314, B:I.316 Hydrogen bonds: B:Y.200, A:N.101 DN0.17: 32 residues within 4Å: Chain C: N.101, S.178, T.179, A.180, E.183, Y.224 Chain D: I.4, Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, C.239, L.240, L.246, N.247, A.248, L.250, K.252, L.253, N.256, M.257, A.314, I.316, K.350, T.351, A.352, I.368 Ligands: GTP.11 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Q.134, D:N.165, D:F.167, D:F.167, D:Y.200, D:T.237, D:L.240, D:L.246, D:L.250, D:L.253, D:L.253, D:A.314, D:I.368 Hydrogen bonds: D:Y.200, C:N.101

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

ACP.20: 24 residues within 4Å: Chain F: K.74, P.95, I.148, K.150, K.156, Q.183, K.184, Y.185, L.186, K.198, F.199, 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 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.150, F:K.156, F:K.184, F:Y.185, F:L.186, F:K.198, F:D.200, F:R.202, F:T.241, F:T.241, F:N.242, F:N.333, F:N.333 Salt bridges: F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, L. et al., Reversible binding of the anticancer drug KXO1 (tirbanibulin) to the colchicine-binding site of beta-tubulin explains KXO1's low clinical toxicity. J.Biol.Chem. (2019)

Release Date

2019-10-23

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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