SMTL ID : 8clg.1

Epothilone A and Colchicine bound to tubulin (T2R-TTL) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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.143, G.144, T.145, G.146, I.171, V.177, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B 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.144, A:T.145, A:G.146, A:S.178, A:S.178, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:D.98, A:F.141, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.10: 23 residues within 4Å: Chain C: 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, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.11 31 PLIP interactions: 26 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.143, 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:G.13, C:F.141, C:T.145, C:T.145, C:E.183, D:K.252, D:K.252, 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: 3 residues within 4Å: Chain A: D.69, E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: Q.11, N.99, D.177 Ligands: GDP.8 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: Q.11, D.69, E.71 Ligands: GTP.10 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.69, H2O.1, H2O.1, H2O.1 MG.15: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.14 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.39, T.41, G.44, 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: 1 residues within 4Å: Chain B: D.118 No protein-ligand interaction detected (PLIP) CA.5: 1 residues within 4Å: Chain B: E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.12: 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:D.39, C:G.44, C:E.55, C:E.55

2 x EP: EPOTHILONE A(Non-covalent)

EP.6: 17 residues within 4Å: Chain B: L.215, L.217, D.224, H.227, L.228, A.231, F.270, P.272, L.273, T.274, S.275, R.276, Q.279, Q.280, R.282, L.284, L.361 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.215, B:L.217, B:L.228, B:P.272, B:L.273, B:L.284, B:L.361 Hydrogen bonds: B:D.224, B:T.274 EP.13: 16 residues within 4Å: Chain D: L.215, L.217, G.223, D.224, H.227, L.228, A.231, F.270, P.272, L.273, T.274, S.275, R.276, Q.279, R.282, L.361 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.217, D:H.227, D:T.274, D:R.276, D:Q.279, D:L.361 Hydrogen bonds: D:D.224, D:T.274, D:Q.279

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

LOC.7: 24 residues within 4Å: Chain A: N.101, S.178, T.179, A.180, V.181 Chain B: 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, A.315, I.316, N.348, K.350, A.352, I.368 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:V.181 Hydrophobic interactions: B:A.248, B:K.252, B:L.253, B:L.253, B:A.314, B:K.350, B:K.350 Water bridges: B:N.256

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

GDP.8: 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.9 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:N.99, 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:G.141 pi-Stacking: B:Y.222, B:Y.222 GDP.14: 19 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, N.99, S.138, G.140, 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 ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.16: 16 residues within 4Å: Chain F: K.74, I.129, K.131, K.137, G.138, Q.164, K.165, Y.166, L.167, K.179, D.181, L.221, T.222, M.301, I.311, E.312 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.74, F:K.165, F:L.167, F:K.179, F:D.181, F:T.222, F:T.222, F:E.312 Salt bridges: F:K.74, F:K.131

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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