SMTL ID : 5yls.1

Crystal structure of T2R-TTL-Y50 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, 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, L.227, N.228, I.231 Ligands: MG.2 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.98, A:D.98, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, 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:T.145, A:T.145, B:K.252, B:K.252 pi-Stacking: A:Y.224 Salt bridges: B:K.252 GTP.9: 25 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.143, G.144, T.145, G.146, I.171, V.177, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Ligands: MG.10 25 PLIP interactions: 22 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:D.98, 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:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:T.145, C:T.145, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252 GTP.12: 20 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.13 21 PLIP interactions: 21 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:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:G.144, D:S.176, D:S.176, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

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

MG.2: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain D: Q.11, D.67, E.69 Ligands: GTP.12 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.39, T.41, G.44, D.47, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:T.41, A:T.41, A:G.44, A:E.55 CA.11: 6 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, D.47, E.55 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.39, C:D.39, C:T.41, C:G.44, C:E.55

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.216, P.274, V.275, I.276, A.294, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.275, A:V.275, A:N.300

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

GDP.5: 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.6 19 PLIP interactions: 19 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:N.99, B:T.143, B:T.143, B:D.177 pi-Stacking: B:Y.222, B:Y.222

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

MES.7: 9 residues within 4Å: Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, D.197, R.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.156 Salt bridges: B:D.197, B:R.251

2 x Y50: E-3-(3-azanyl-4-methoxy-phenyl)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)prop-2-en-1-one(Non-covalent)

Y50.8: 20 residues within 4Å: Chain A: T.179, A.180, V.181 Chain B: Y.200, V.236, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, N.348, K.350, A.352, I.368 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.240, B:A.248, B:L.253, B:L.253, B:N.256, B:K.350, B:K.350 Hydrogen bonds: B:D.249, A:T.179 Y50.14: 20 residues within 4Å: Chain C: T.179, A.180, V.181 Chain D: Y.200, V.236, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, I.316, N.348, K.350, A.352, I.368 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.240, D:A.248, D:L.253, D:N.256, D:I.316 Hydrogen bonds: D:D.249, C:T.179, C:V.181

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

ACP.15: 18 residues within 4Å: Chain F: K.74, I.148, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.74, F:K.184, F:L.186, F:K.198, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:N.242, F:N.333, F:N.333, F:N.333 Salt bridges: F:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J.H. et al., The compound millepachine and its derivatives inhibit tubulin polymerization by irreversibly binding to the colchicine-binding site in beta-tubulin. J. Biol. Chem. (2018)

Release Date

2018-04-11

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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