SMTL ID : 5s51.1

Tubulin-Z1251207602-complex

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.142, 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 32 PLIP interactions: 27 interactions with chain A, 5 interactions with chain B Hydrogen bonds: 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:S.140, A:G.144, A:T.145, A:G.146, A:S.178, A:T.179, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:Q.11, A:S.140, A:F.141, A:G.142, A:T.145, A:T.145, A:A.174, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224 Salt bridges: B:K.252, 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: 25 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, C:D.98, C:D.98, 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:E.71, C:G.142, C:T.145, C:T.145, 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: Q.11, 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, N.99 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: D.98 Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.14 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.331, 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.4: 2 residues within 4Å: Chain A: S.158 Chain E: D.42 No protein-ligand interaction detected (PLIP) 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: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:T.41, C:G.44, C:E.55, H2O.4

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 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:Q.15, 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:D.67, B:A.97, B:S.138, B:L.139, B:T.143, B:S.145, 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, N.99, 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: MG.15 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, 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

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

MES.8: 10 residues within 4Å: Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, T.196, D.197, R.251 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:D.197, B:R.251 Water bridges: A:E.411

2 x RWS: 1-(5-methyl-1,3,4-thiadiazol-2-yl)piperidine(Non-covalent)

RWS.9: 13 residues within 4Å: Chain B: E.198, Y.200, V.236, C.239, L.253, A.314, A.315, I.316, K.350, T.351, A.352, I.368 Ligands: RWS.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.253, B:A.314, B:I.316, B:K.350, B:A.352 RWS.10: 17 residues within 4Å: Chain A: N.101, T.179, A.180, V.181 Chain B: L.246, A.248, K.252, L.253, N.256, M.257, T.312, V.313, A.314, N.347, N.348, K.350 Ligands: RWS.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.252, B:K.350, B:K.350, A:V.181

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

ACP.16: 19 residues within 4Å: Chain F: K.74, I.148, K.150, A.155, Q.183, K.184, Y.185, L.186, K.198, D.200, R.222, H.239, T.241, N.242, D.318, M.320, E.331, N.333 Ligands: MG.17 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, F:Q.183, 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: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

Muhlethaler, T. et al., Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2021-06-30

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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