SMTL ID : 7en3.1

Crystal structure of tubulin in complex with Tubulysin analogue TGL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 25 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.143, G.144, T.145, G.146, I.171, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 30 PLIP interactions: 27 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:A.99, A:N.101, A:N.101, A:S.140, A:G.143, A:G.144, 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:Q.11, A:Q.11, A:G.13, A:F.141, A:T.145, A:T.145, A:A.174, A:E.183, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.10: 26 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, P.173, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.11 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:N.101, C:S.140, C:G.143, 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:G.13, C:E.71, C:F.141, C:T.145, C:T.145, 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

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: Q.11, E.69 Ligands: GDP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.69, H2O.2, H2O.3, H2O.4 MG.11: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.10 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, G.45, 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.12: 4 residues within 4Å: Chain C: D.39, T.41, G.44, 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

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

GDP.4: 20 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.5, J6R.8 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:S.176, 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:V.175, B:S.176, B:S.176 pi-Stacking: B:Y.222, B:Y.222 GDP.13: 17 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:S.176, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:G.13, D:E.69 pi-Stacking: D:Y.222, D:Y.222

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

MES.6: 9 residues within 4Å: Chain B: R.156, P.160, D.161, R.162, M.164, N.195, T.196, D.197, R.251 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.197, B:R.251 MES.7: 10 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, P.305, R.306, Y.310, V.333, N.337, Y.340 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.296 Salt bridges: B:R.306 MES.9: 7 residues within 4Å: Chain C: Y.262, P.263, R.264, I.265, D.431, E.434, V.435 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.264, C:I.265 Salt bridges: C:D.431 pi-Cation interactions: C:Y.262

2 x J6R: (2S,4R)-5-(4-fluorophenyl)-2-methyl-4-[[2-[(1R,3R)-4-methyl-3-[5-methylhexyl-[(2S,3S)-3-methyl-2-[[(2R)-1-methylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-1-oxidanyl-pentyl]-1,3-thiazol-4-yl]carbonylamino]pentanoic acid(Non-covalent)

J6R.8: 23 residues within 4Å: Chain B: Q.11, Q.15, P.173, K.174, V.175, D.177, P.220, T.221, Y.222, G.223, L.225, R.276 Chain C: A.247, L.248, V.250, P.325, V.328, N.329, I.332, F.351, V.353, I.355 Ligands: GDP.4 20 PLIP interactions: 11 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:Q.15, B:V.175, B:Y.222, B:L.225, C:L.248, C:V.250, C:P.325, C:V.328, C:I.332, C:V.353, C:I.355 Hydrogen bonds: B:P.220, B:T.221, B:Y.222, B:G.223, C:N.329, C:N.329 Salt bridges: B:D.177, B:R.276 Halogen bonds: B:Q.11 J6R.14: 12 residues within 4Å: Chain D: Q.11, Q.15, P.173, K.174, V.175, S.176, D.177, P.220, T.221, Y.222, G.223, R.276 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Q.15, D:V.175, D:Y.222, D:Y.222, D:Y.222 Hydrogen bonds: D:P.220, D:T.221, D:Y.222, D:G.223 Salt bridges: D:D.177, D:R.276 Halogen bonds: D:Q.11

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, H.239, L.240, T.241, N.242, D.318, I.330, E.331, N.333 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:K.74, F:Q.183, F:L.186, F:K.198, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:T.241, F:D.318, F:E.331, F:N.333, F:N.333 Salt bridges: F:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., The X-ray structure of tubulysin analogue TGL in complex with tubulin and three possible routes for the development of next-generation tubulysin analogues. Biochem.Biophys.Res.Commun. (2021)

Release Date

2022-04-27

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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