SMTL ID : 7daf.1

IXA in complex with tubulin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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.143, G.144, T.145, G.146, I.171, V.177, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 29 PLIP interactions: 25 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:D.98, A:A.99, 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:N.101, A:S.140, A:F.141, A:T.145, A:T.145, A:A.174, A:E.183, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.11: 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.12 30 PLIP interactions: 5 interactions with chain D, 25 interactions with chain C Water bridges: D:K.252, D:K.252, D:K.252, D:K.252, C:G.13, C:F.141, C:T.145, C:T.145, C:T.179, C:E.183 Salt bridges: D:K.252 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 pi-Stacking: C:Y.224, C:Y.224

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

MG.2: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: D.69 Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: Q.11, N.99 Ligands: GDP.14 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain A: E.450 Chain F: K.74, E.331, N.333 Ligands: ACP.19 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, D.47, 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.7: 1 residues within 4Å: Chain B: E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.13: 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 CA.17: 2 residues within 4Å: Chain A: E.196 Chain E: D.42 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: E:D.42, A:E.196, H2O.4, H2O.5

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: Y.161, G.162, K.163, K.164 Ligand excluded by PLIP

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

GDP.5: 18 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, Y.222, N.226 Ligands: MG.6 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:V.175, B:D.177, 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:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.14: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.15 17 PLIP interactions: 17 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:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:E.69, D:E.69, D:S.138, D:G.140

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

MES.8: 10 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 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.156, B:R.251 Salt bridges: B:D.197, B:R.251 MES.9: 8 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, R.306, N.337, Y.340, F.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.296 Salt bridges: B:R.306

1 x GZX: (1~{S},3~{S},7~{S},10~{R},11~{S},12~{S},16~{R})-8,8,10,12,16-pentamethyl-3-[(~{E})-1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl]-7,11-bis(oxidanyl)-17-oxa-4-azabicyclo[14.1.0]heptadecane-5,9-dione(Non-covalent)

GZX.16: 15 residues within 4Å: Chain D: L.215, L.217, D.224, H.227, L.228, A.231, F.270, P.272, L.273, T.274, R.276, Q.279, R.282, L.284, L.361 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.215, D:L.215, D:H.227, D:L.228, D:A.231, D:F.270, D:P.272, D:L.273, D:R.276, D:R.282, D:L.361 Hydrogen bonds: D:T.274, D:Q.279

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

ACP.19: 20 residues within 4Å: Chain A: E.450 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, T.241, N.242, D.318, I.330, E.331, N.333 Ligands: MG.18 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:K.74, F:Q.183, F:L.186, F:K.198, F:D.200, F:R.202, F:R.222, F:T.241, F:T.241, F:N.242, F:N.242, F:E.331, F:N.333, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, Q. et al., High-resolution X-ray structure of three microtubule-stabilizing agents in complex with tubulin provide a rationale for drug design. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-03-24

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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