SMTL ID : 8cle.1

Vinblastine bound to tubulin (T2R-TTL) complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 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.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 F: K.252 Ligands: MG.2 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.98, A:A.99, A:A.100, A:N.101, A:S.140, A:G.143, 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 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: F:K.252 GTP.5: 24 residues within 4Å: Chain B: 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 C: K.252 Ligands: MG.6 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.11, B:A.12, B:Q.15, B:D.98, B:A.99, B:N.101, B:S.140, B:G.143, B:G.144, B:T.145, B:G.146, B:V.177, B:E.183, B:N.206, B:N.206, B:N.228, B:N.228 pi-Stacking: B:Y.224, B:Y.224 Salt bridges: C:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: D.69, E.71 Ligands: GTP.5 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, F.49, 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: 5 residues within 4Å: Chain B: D.39, T.41, G.44, D.47, E.55 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.39, B:D.39, B:T.41, B:E.55, B:E.55

1 x VLB: (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE(Non-covalent)

VLB.4: 22 residues within 4Å: Chain B: L.248, P.325, V.328, N.329, I.332, A.333, F.351, V.353, G.354, I.355 Chain F: P.173, K.174, V.175, S.176, D.177, Y.208, T.218, T.219, P.220, T.221, Y.222, L.225 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain F Hydrophobic interactions: B:L.248, B:P.325, B:P.325, B:V.328, B:I.332, B:I.332, B:F.351, B:V.353, B:I.355, F:V.175, F:Y.222, F:L.225 Hydrogen bonds: B:N.329, B:N.329, F:P.220 Salt bridges: F:D.177

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

GDP.8: 17 residues within 4Å: Chain C: G.10, Q.11, C.12, Q.15, 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 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Q.11, C:Q.11, C:C.12, C:N.99, C:S.138, C:G.141, C:G.142, C:T.143, C:T.143, C:G.144, C:S.176, C:E.181, C:N.204, C:N.204, C:N.226, C:N.226 GDP.9: 18 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:S.138, F:G.142, F:T.143, F:T.143, F:G.144, F:S.176, F:S.176, F:E.181, F:N.204, F:N.204, F:N.226, F:N.226 pi-Stacking: F:Y.222

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: AB
Tubulin beta-2B chain: CF
Stathmin-4: D
Tubulin-Tyrosine Ligase: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

F
B

D
E

E
F

Tubulin alpha-1B chain

Tubulin beta-2B chain

Stathmin-4

Tubulin-Tyrosine Ligase

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