SMTL ID : 6fkj.1

Tubulin-TUB075 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 24 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, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 35 PLIP interactions: 29 interactions with chain A, 6 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:G.146, A:V.177, A:S.178, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:G.142, A:T.145, A:T.145, A:A.174, A:E.183, B:K.252, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, 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, S.178, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.14 33 PLIP interactions: 28 interactions with chain C, 5 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:N.101, C:S.140, C:G.144, C:T.145, C:G.146, C:V.177, C:S.178, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:E.71, C:S.140, C:G.142, C:T.145, C:T.145, C:A.174, 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, D:K.252

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.69, E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.6 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.18: 3 residues within 4Å: Chain D: Q.11, D.177 Ligands: GDP.17 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

5 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

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:D.39, A:T.41, A:G.44, H2O.1 CA.8: 2 residues within 4Å: Chain B: E.108, E.111 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.111, H2O.7, H2O.10 CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.15: 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:T.41, C:G.44, C:E.55, C:E.55 CA.19: 2 residues within 4Å: Chain A: S.158 Chain E: D.42 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.216, P.274, V.275, L.286, A.294, N.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.216, A:V.275 GOL.10: 4 residues within 4Å: Chain B: S.176, P.220, T.221, Y.222 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.176, B:P.220 Water bridges: B:S.176, B:Y.222

2 x DLW: (5~{S})-2-[(~{E})-~{N}-(2-ethoxyphenyl)-~{C}-methyl-carbonimidoyl]-3-oxidanyl-5-phenyl-cyclohex-2-en-1-one(Non-covalent)

DLW.5: 21 residues within 4Å: Chain A: T.179 Chain B: Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, L.240, L.246, L.250, L.253, N.256, M.257, A.314, A.315, I.316, K.350, T.351, A.352 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:N.165, B:F.167, B:F.167, B:Y.200, B:V.236, B:T.237, B:L.240, B:L.246, B:L.250, B:L.253, B:N.256, B:A.314, B:I.316, B:K.350, B:A.352 Hydrogen bonds: B:Y.200 DLW.16: 21 residues within 4Å: Chain C: T.179 Chain D: Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, L.240, L.246, L.250, L.253, N.256, M.257, A.314, A.315, I.316, K.350, T.351, A.352 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:N.165, D:F.167, D:F.167, D:Y.200, D:V.236, D:T.237, D:L.240, D:L.246, D:L.250, D:N.256, D:A.314, D:I.316, D:K.350, D:A.352 Hydrogen bonds: D:Y.200, D:L.253

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

GDP.6: 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.7 23 PLIP interactions: 23 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:A.97, B:S.138, B:G.140, B:T.143, B:S.145, B:S.145, B:D.177 pi-Stacking: B:Y.222, B:Y.222 GDP.17: 21 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, N.99, 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.18 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:V.175, D:E.181, 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

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

MES.11: 10 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, N.195, T.196, D.197, R.251 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.197, B:R.251

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 6 residues within 4Å: Chain B: R.390, R.391, K.392, H.396 Chain C: Y.262, P.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.390 Water bridges: B:H.396, B:T.399

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

ACP.21: 20 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, M.320, E.331, N.333 Ligands: MG.20 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, 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:N.242, F:D.318, F:D.318, F:N.333, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bueno, O. et al., High-affinity ligands of the colchicine domain in tubulin based on a structure-guided design. Sci Rep (2018)

Release Date

2018-03-21

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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