SMTL ID : 8clb.1

Colchicine bound to tubulin (T2R-TTL) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 31 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, N.102, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 27 PLIP interactions: 22 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:D.98, A:D.98, A:A.99, A:N.101, A:N.101, A:G.143, A:G.144, A:T.145, A:T.145, A:G.146, A:N.206, A:N.206, A:Y.224, A:Y.224, A:N.228, A:N.228 Water bridges: A:G.13, A:S.140, B:K.252, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224 Salt bridges: B:K.252 GTP.7: 28 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.8 27 PLIP interactions: 24 interactions with chain C, 3 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.143, C:G.144, C:T.145, C:T.145, C:G.146, C:S.178, C:S.178, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:G.142, C:E.183, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: Q.11, D.69, E.71 Chain B: N.247, K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: Q.11, N.99, D.177 Ligands: GDP.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.177, H2O.1 MG.8: 5 residues within 4Å: Chain C: Q.11, D.69, E.71, D.98 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain D: Q.11, N.99, D.177 Ligands: GDP.10 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, F.49, N.50, E.55, H.61 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.9: 7 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, F.49, E.55, H.61 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: 28 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.5 15 PLIP interactions: 15 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:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.10: 29 residues within 4Å: Chain D: G.10, Q.11, C.12, G.13, Q.15, I.16, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.11 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.141, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

2 x LOC: N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide(Non-covalent)

LOC.6: 21 residues within 4Å: Chain A: S.178, T.179, A.180, V.181 Chain B: C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.348, K.350, A.352, I.368 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.248, B:K.252, B:L.253, B:N.256, B:A.314, B:K.350 Hydrogen bonds: A:V.181 LOC.12: 22 residues within 4Å: Chain C: S.178, T.179, A.180, V.181 Chain D: V.236, C.239, L.240, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.348, K.350, A.352, I.368 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.246, D:L.246, D:A.248, D:K.252, D:L.253, D:L.253, D:A.314, D:K.350 Hydrogen bonds: D:K.350, C:V.181

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

ACP.13: 19 residues within 4Å: Chain F: K.74, P.95, I.119, Q.139, K.140, Y.141, L.142, K.154, D.156, R.178, H.192, L.193, T.194, N.195, D.270, M.272, I.282, E.283, N.285 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:K.74, F:K.140, F:L.142, F:K.154, F:R.178, F:T.194, F:T.194, F:N.195, F:D.270, F:E.283, F:N.285 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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