SMTL ID : 5jh7.1

Tubulin-Eribulin complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 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, D.69, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:A.99, A:A.100, A:N.101, A:S.140, 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:G.13, A:F.141, A:T.145, A:T.145, A:A.174, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.13: 24 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, 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, N.228, I.231 Chain D: K.252 Ligands: MG.14 29 PLIP interactions: 25 interactions with chain C, 4 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: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:G.13, C:E.71, C:F.141, C:T.145, C:T.145, C:T.179, 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: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.21 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.331, F:E.331, H2O.25

5 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:T.41, A:T.41, A:E.55, H2O.1 CA.7: 1 residues within 4Å: Chain B: E.111 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.111, H2O.8 CA.15: 4 residues within 4Å: Chain C: D.39, T.41, G.44, 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.12 CA.16: 2 residues within 4Å: Chain C: D.218, E.220 No protein-ligand interaction detected (PLIP) CA.20: 2 residues within 4Å: Chain A: E.196 Chain E: D.42 No protein-ligand interaction detected (PLIP)

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 5 residues within 4Å: Chain A: N.216, P.274, V.275, A.294, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.275, A:N.300 Water bridges: A:N.216 IMD.11: 5 residues within 4Å: Chain B: F.294, R.306, N.337, Y.340 Ligands: IMD.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.306 IMD.12: 5 residues within 4Å: Chain B: F.294, D.295, S.296, R.306 Ligands: IMD.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.295, B:S.296, B:R.306 pi-Cation interactions: B:R.306

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: R.105, T.109, G.410, E.411 Chain B: D.161 Chain E: R.59 Ligands: MES.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.105, A:G.410, B:D.161 Water bridges: B:D.161 GOL.17: 8 residues within 4Å: Chain C: C.4, Q.133, G.134, S.165, L.167, L.242, T.253, Q.256 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.134, C:S.165, C:Q.256

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

GDP.6: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, S.138, G.141, G.142, T.143, G.144, V.169, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: 6K9.8, 03S.9 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.13, B:E.69, B:A.97, B:L.139, B:G.141, B:T.143, B:S.145, B:S.172, B:S.176, B:S.176 GDP.18: 19 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, S.138, G.141, G.142, T.143, G.144, V.169, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: 6K9.19 22 PLIP interactions: 22 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:Y.222, D:N.226, D:N.226 Water bridges: D:S.138, D:S.138, D:G.140, D:T.143, D:S.145, D:S.145, D:S.176

2 x 6K9: (1S,3S,6S,9S,12S,14R,16R,18S,20R,21R,22S,26R,29S,31R,32S,33R,35R,36S)-20-[(2S)-3-amino-2-hydroxypropyl]-21-methoxy-14-methyl-8,15-dimethylidene-2,19,30,34,37,39,40,41-octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6,9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-24-one (non-preferred name)(Non-covalent)

6K9.8: 26 residues within 4Å: Chain B: Q.11, N.99, P.173, K.174, V.175, S.176, D.177, T.178, E.181, Y.208, P.220, T.221, Y.222, L.225 Chain C: A.247, L.248, N.249, V.250, E.254, N.329, I.332, F.351, K.352, V.353 Ligands: GDP.6, 03S.9 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:V.175, B:Y.208, B:Y.222, B:Y.222, B:L.225, C:V.250 Hydrogen bonds: B:D.177, B:Y.222, C:N.329, C:F.351, C:F.351 Water bridges: B:N.99, B:S.176, B:S.176, C:N.329, C:V.353 6K9.19: 15 residues within 4Å: Chain D: Q.11, N.99, P.173, K.174, V.175, S.176, D.177, T.178, E.181, Y.208, P.220, T.221, Y.222, L.225 Ligands: GDP.18 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.222, D:Y.222, D:Y.222, D:L.225 Hydrogen bonds: D:D.177, D:D.177, D:Y.222

1 x 03S: methanesulfonic acid(Non-covalent)

03S.9: 5 residues within 4Å: Chain B: Q.11, E.69, N.99 Ligands: GDP.6, 6K9.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.69, B:N.99 Water bridges: B:E.69, B:A.97, B:G.98, B:G.142, B:T.143

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

MES.10: 11 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, M.164, N.195, T.196, D.197, R.251 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.197, B:R.251

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

ACP.21: 19 residues within 4Å: Chain F: K.74, I.148, K.150, 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, E.331, N.333 Ligands: MG.22 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, F:K.184, F:L.186, F:K.198, F:D.200, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:D.318, F:D.318, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doodhi, H. et al., Termination of Protofilament Elongation by Eribulin Induces Lattice Defects that Promote Microtubule Catastrophes. Curr.Biol. (2016)

Release Date

2016-06-29

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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