SMTL ID : 6eg5.1

The structure of SB-1-202-tubulin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

3 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.142, 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.252 Ligands: MG.2 28 PLIP interactions: 26 interactions with chain A, 2 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:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:S.140, A:F.141, A:T.145, A:T.145, A:A.174, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.13: 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, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.14 29 PLIP interactions: 27 interactions with chain C, 2 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.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:E.71, C:E.71, C:E.71, C:F.141, C:T.145, C:T.179, C:E.183, D:K.252 pi-Stacking: C:Y.224 Salt bridges: D:K.252 GTP.16: 24 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.17 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:S.138, D:G.141, 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 Water bridges: D:S.138, D:S.138 pi-Stacking: D:Y.222, D:Y.222

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.7 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain D: Q.11, E.69 Ligands: GTP.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.69 MG.20: 3 residues within 4Å: Chain F: D.318, E.331 Ligands: ACP.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.318 MG.21: 4 residues within 4Å: Chain F: S.152, E.331, N.333 Ligands: ACP.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

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.9: 1 residues within 4Å: Chain B: E.111 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.111, H2O.11 CA.15: 4 residues within 4Å: Chain C: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:G.44, C:E.55, C:E.55, H2O.14 CA.19: 1 residues within 4Å: Chain E: D.42 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: Y.161, G.162, K.163, K.164 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: N.216, A.273, P.274, V.275, I.276, L.286, A.294, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.216, A:V.275 Water bridges: A:N.300 GOL.6: 4 residues within 4Å: Chain A: Y.262, P.263, R.264, D.431 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.264

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

GDP.7: 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.8 21 PLIP interactions: 21 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:V.175, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:A.97, B:S.138, B:L.139, B:G.141, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.10: 10 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, N.195, T.196, D.197, R.251 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:R.105, B:R.156, B:R.251 Salt bridges: B:D.197, B:R.251 MES.11: 8 residues within 4Å: Chain B: F.294, D.295, S.296, R.306, Y.310, V.333, N.337, Y.340 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.296 Salt bridges: B:R.306

2 x J7S: 4-(2-chloropyrido[2,3-d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one(Non-covalent)

J7S.12: 16 residues within 4Å: Chain A: T.179, V.181 Chain B: C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, A.315, I.316, K.350, A.352 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.246, B:N.256, B:A.314, B:A.314, B:K.350 Hydrogen bonds: B:N.256, A:T.179 J7S.18: 17 residues within 4Å: Chain C: N.101, T.179, V.181 Chain D: C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, V.313, A.314, A.315, I.316, K.350, A.352 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.246, D:A.314, D:A.314, D:K.350, D:A.352 Hydrogen bonds: D:N.256, C:T.179

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

ACP.22: 21 residues within 4Å: Chain F: K.74, K.150, A.155, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, H.239, L.240, T.241, N.242, D.318, I.330, E.331, N.333 Ligands: MG.20, MG.21 18 PLIP interactions: 18 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:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:T.241, F:N.242, F:E.331, F:N.333, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, H. et al., The structure of SB-1-202/SB-2-204-tubulin complex. To Be Published

Release Date

2019-08-21

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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