SMTL ID : 8clc.1

Tubulin (T2R-TTL) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 23 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, E.183, N.206, Y.224, N.228, I.231 Chain B: K.251 Ligands: MG.2 24 PLIP interactions: 22 interactions with chain A, 2 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.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:E.71, A:T.145, A:T.145, A:A.174, B:K.251 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.251 GTP.6: 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.251 Ligands: MG.7 26 PLIP interactions: 23 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, 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:F.141, C:T.145, C:T.145, D:K.251, D:K.251 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.251

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11 Chain B: K.251 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: Q.10, N.98, D.176 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain C: E.71, D.98 Chain D: K.251 Ligands: GTP.6 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.39, T.41, G.44, D.47, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:D.39, A:T.41, A:E.55, A:E.55 CA.8: 5 residues within 4Å: Chain C: D.39, T.41, G.44, D.47, 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

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

GDP.4: 18 residues within 4Å: Chain B: G.9, Q.10, C.11, Q.14, S.137, G.140, G.141, T.142, G.143, P.170, V.174, D.176, E.180, N.203, L.206, Y.221, N.225 Ligands: MG.5 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:Q.10, B:C.11, B:S.137, B:G.141, B:T.142, B:T.142, B:G.143, B:D.176, B:E.180, B:N.203, B:N.203, B:N.225, B:N.225 Water bridges: B:G.12, B:A.96, B:L.138, B:G.140, B:T.142, B:T.142, B:S.144 pi-Stacking: B:Y.221, B:Y.221 GDP.9: 18 residues within 4Å: Chain D: G.9, Q.10, C.11, Q.14, N.98, S.137, G.139, G.140, G.141, T.142, G.143, P.170, V.174, D.176, E.180, N.203, Y.221, N.225 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.10, D:Q.10, D:C.11, D:S.137, D:G.141, D:T.142, D:T.142, D:T.142, D:G.143, D:V.174, D:E.180, D:N.203, D:N.203, D:N.225, D:N.225 pi-Stacking: D:Y.221, D:Y.221

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

ACP.10: 19 residues within 4Å: Chain F: K.74, I.126, G.132, Q.155, K.156, Y.157, L.158, K.170, D.172, R.174, H.208, L.209, T.210, N.211, D.278, M.280, I.290, E.291, N.293 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.74, F:G.132, F:Q.155, F:L.158, F:K.170, F:D.172, F:R.174, F:T.210, F:D.278, F:D.278, F:D.278, F:E.291, F:N.293 Salt bridges: F:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wranik, M. et al., A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers. Nat Commun (2023)

Release Date

2023-12-13

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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