SMTL ID : 8clh.1

Drug cocktail (Colchicine, Epothilone A, Peloruside, Ansamitocin P3, Vinblastine) bound to tubulin (T2R-TTL) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 24 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, E.183, N.206, Y.224, N.228, I.231 Chain B: K.251 Ligands: MG.2 30 PLIP interactions: 27 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:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, 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:F.141, A:T.145, A:T.145, B:K.251, B:K.251 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.251 GTP.10: 25 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: Q.244, K.251 Ligands: MG.11 28 PLIP interactions: 24 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, 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:E.71, C:S.140, C:F.141, C:T.145, C:T.145, C:E.183, D:K.251, D:K.251, D:K.251 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.251

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: K.251 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: Q.10, N.98 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: E.71, D.98 Ligands: GTP.10 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain D: Q.10, N.98 Ligands: GDP.13 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:G.44, A:E.55 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: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, V.168, P.170, V.174, S.175, E.180, N.203, Y.221, N.225 Ligands: MG.5 23 PLIP interactions: 23 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:E.180, B:N.203, B:N.203, B:N.225, B:N.225 Water bridges: B:Q.10, B:Q.10, B:A.96, B:N.98, B:S.137, B:G.139, B:G.140, B:T.142, B:S.144 pi-Stacking: B:Y.221, B:Y.221 GDP.13: 18 residues within 4Å: Chain D: G.9, Q.10, C.11, Q.14, S.137, G.140, G.141, T.142, G.143, V.168, P.170, V.174, S.175, E.180, N.203, Y.221, N.225 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.10, D:C.11, D:S.137, D:G.140, D:G.141, D:T.142, D:T.142, D:G.143, D:E.180, D:N.203, D:N.203, D:N.225, D:N.225 Water bridges: D:G.139, D:S.144

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.6: 23 residues within 4Å: Chain A: N.101, S.178, T.179, A.180, V.181 Chain B: C.238, L.239, L.245, A.247, D.248, K.251, L.252, N.255, M.256, T.311, V.312, A.313, A.314, I.315, N.347, K.349, T.350, A.351 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.247, B:K.251, B:L.252, B:N.255, B:A.313 Hydrogen bonds: A:V.181

2 x EP: EPOTHILONE A(Non-covalent)

EP.7: 17 residues within 4Å: Chain B: L.214, L.216, D.223, H.226, L.227, A.230, F.269, P.271, L.272, T.273, R.275, Q.278, Q.279, Y.280, R.281, L.283, L.360 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.216, B:L.227, B:P.271, B:L.272, B:R.275, B:L.360 Hydrogen bonds: B:D.223 EP.15: 15 residues within 4Å: Chain D: L.214, L.216, D.223, H.226, L.227, A.230, F.269, P.271, L.272, T.273, S.274, R.275, Q.278, R.281, L.360 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.214, D:L.214, D:L.227, D:F.269, D:P.271, D:L.272, D:T.273, D:R.275, D:L.360 Hydrogen bonds: D:D.223, D:T.273, D:Q.278

1 x POU: Peloruside A(Non-covalent)

POU.8: 12 residues within 4Å: Chain B: T.289, Q.290, F.293, D.294, S.295, K.296, P.304, R.305, Y.309, V.332, N.336, Y.339 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.305, B:Y.339, B:Y.339 Hydrogen bonds: B:F.293, B:S.295

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

VLB.9: 24 residues within 4Å: Chain B: P.172, K.173, V.174, S.175, D.176, Y.207, F.211, T.217, T.218, P.219, T.220, Y.221, L.224 Chain C: L.248, P.325, V.328, N.329, I.332, A.333, K.336, F.351, V.353, G.354, I.355 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:P.325, C:V.328, C:I.332, C:I.332, C:F.351, C:V.353, C:I.355, B:Y.221, B:L.224 Hydrogen bonds: C:N.329, C:N.329, B:P.219 Salt bridges: B:D.176

1 x BKF: (1S,2S,3S,5S,6S,16Z,18Z,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl 2-methylpropanoate(Non-covalent)

BKF.16: 11 residues within 4Å: Chain D: G.97, N.98, N.99, K.102, D.176, T.177, V.178, V.179, F.393, W.396, Y.397 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.177, D:F.393, D:W.396, D:W.396, D:Y.397 Hydrogen bonds: D:N.98, D:N.99

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

ACP.17: 17 residues within 4Å: Chain F: K.74, I.148, K.150, Q.183, K.184, Y.185, L.186, K.198, D.200, H.239, L.240, T.241, D.318, M.320, I.330, E.331, N.333 16 PLIP interactions: 16 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:T.241, F:T.241, F:N.242, F:D.318, F:D.318, F:E.331, F:E.331, F:N.333 Salt bridges: F:K.74, F:K.150

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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