SMTL ID : 8wmu.1

Structural basis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents with dual-binding sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

3 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 Ligands: MG.2, 01.9 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:D.98, A:A.99, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:S.178, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224 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, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.11 23 PLIP interactions: 22 interactions with chain C, 1 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:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 Water bridges: C:G.13 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252 GTP.14: 19 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, S.176, E.181, N.204, L.207, Y.222, N.226 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:A.97, D:N.99, D:S.138, D:G.141, D:G.142, 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

3 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.7: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.6 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.10 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, N.50, 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.216, P.274, V.275, I.276, L.286, A.294, N.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.275, A:V.275

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain A: V.177, T.223, Y.224 Chain B: Q.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.177, A:Y.224

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

GDP.6: 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.7 20 PLIP interactions: 20 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:T.143, B:G.144, B:V.175, B:D.177, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 Water bridges: B:G.141, B:S.145 pi-Stacking: B:Y.222, B:Y.222

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

MES.8: 9 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, N.195, T.196, D.197, R.251 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.197, B:R.251

1 x 01: (5~{S},5~{a}~{S},8~{a}~{R},9~{R})-5-(quinolin-6-ylamino)-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one

01.9: 25 residues within 4Å: Chain A: N.101, S.178, T.179, A.180, Y.224 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, T.351, A.352 Ligands: GTP.1 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:A.180, B:L.246, B:L.246, B:A.248, B:L.253, B:N.256, B:K.350 Hydrogen bonds: A:S.178, A:T.179, B:D.249, B:V.313, B:K.350 Salt bridges: B:K.252

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 4 residues within 4Å: Chain C: S.287, V.288, A.289, D.327 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.288, C:A.289

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

ACP.15: 18 residues within 4Å: Chain F: I.148, 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, M.320, I.330, E.331, N.333 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:Q.183, F:L.186, F:K.198, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:N.242, F:N.242, F:E.331, F:N.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, W., Structural basis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents with dual-binding sites. To Be Published

Release Date

2024-10-09

Peptides

Detyrosinated tubulin alpha-1B chain: AC
Tubulin beta 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

Detyrosinated tubulin alpha-1B chain

Tubulin beta chain

Stathmin-4

Tubulin--tyrosine ligase

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