SMTL ID : 7e4r.1

Crystal structure of tubulin in complex with D-DM1-SMe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 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, 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: K.252 Ligands: MG.2 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, A:A.100, A:N.101, A:S.140, A:G.143, 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:D.98, A:D.98, A:T.179, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224 Salt bridges: B:K.252 GTP.7: 31 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, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: Q.245, K.252 Ligands: MG.8 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:A.99, C:A.100, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:T.145, C:G.146, C:V.177, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:Q.11, C:G.13, C:D.98, C:G.142, D:K.252, D:K.252 pi-Stacking: C:Y.224 Salt bridges: D:K.252 GTP.10: 28 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, G.96, A.97, G.98, N.99, 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.12 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:S.138, D:G.142, D:T.143, D:G.144, D:S.176, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:S.138, D:G.141, D:S.145 pi-Stacking: D:Y.222, D:Y.222

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11 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.8: 6 residues within 4Å: Chain C: Q.11, D.69, E.71, D.98 Chain D: K.252 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain D: Q.11, E.69 Ligands: GTP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.69

2 x CA: CALCIUM ION(Non-covalent)

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.9: 7 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, F.49, N.50, E.55 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:D.39, C:T.41, C:E.55, H2O.5

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

GDP.4: 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.5 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:E.69, B:S.138, B:L.139, B:G.140, B:G.141, B:T.143, B:T.143, B:S.145, B:D.177 pi-Stacking: B:Y.222, B:Y.222

1 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.161 Water bridges: B:R.156, B:R.251 Salt bridges: B:D.197, B:R.251

1 x HZ0: (10E,12E)-86-chloro-14-hydroxy-85,14-dimethoxy-33,2,7,10-tetramethyl-12,6-dioxo-7-aza-1(6,4)-oxazinana-3(2,3)-oxirana-8(1,3)-benzenacyclotetradecaphane-10,12-dien-4-yl N-methyl-N-(3-(methylsulfinothioyl)propanoyl)-D-alaninate(Non-covalent)

HZ0.11: 11 residues within 4Å: Chain D: A.97, G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397, Y.398 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:N.100, D:V.180, D:F.394, D:W.397, D:W.397, D:W.397 Hydrogen bonds: D:N.99, D:N.100, D:K.103, D:V.179

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

ACP.13: 20 residues within 4Å: Chain F: K.74, P.95, 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, M.320, I.330, E.331, N.333 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.74, F:Q.183, F:K.184, F:L.186, F:K.198, F:R.202, F:R.222, F:R.222, F:H.239, F:T.241, F:T.241, 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., C3 ester side chain plays a pivotal role in the antitumor activity of Maytansinoids. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-07-07

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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