SMTL ID : 8r6o.1

Tubulin-4AZA2996 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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.142, 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 B: K.252 Ligands: MG.2 27 PLIP interactions: 25 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:G.13, A:E.71, A:F.141, A:T.145, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.9: 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.142, 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 Ligands: MG.10 27 PLIP interactions: 25 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:G.142, C:T.145, C:T.145, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: Q.11, E.69 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.12 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:T.41, A:T.41, A:E.55, H2O.1 CA.8: 1 residues within 4Å: Chain B: E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.11: 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 GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 20 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, L.207, Y.222, N.226 Ligands: MG.5 23 PLIP interactions: 23 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:D.177, 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, B:Y.222 pi-Stacking: B:Y.222, B:Y.222 GDP.12: 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.13 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: 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 Water bridges: D:G.141, D:S.145 pi-Stacking: D:Y.222, D:Y.222

2 x RME: N6-(4-methylpyridin-2-yl)-N2-(2-morpholinoethyl)-3-nitropyridine-2,6-diamine(Non-covalent)

RME.6: 23 residues within 4Å: Chain A: N.101, T.179, A.180, V.181 Chain B: Y.200, V.236, C.239, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.347, N.348, V.349, K.350, I.368 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.181, B:L.246, B:K.252, B:N.256, B:K.350 Hydrogen bonds: A:T.179 Water bridges: B:K.350, B:K.350 RME.14: 23 residues within 4Å: Chain C: N.101, T.179, A.180, V.181 Chain D: Y.200, V.236, C.239, L.246, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.347, N.348, V.349, K.350, I.368 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.246, D:K.252, D:N.256, D:K.350, C:V.181 Water bridges: D:K.350, D:K.350 Hydrogen bonds: C:T.179

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

MES.7: 11 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, T.196, D.197, R.251 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.156 Salt bridges: B:D.197, B:R.251

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

ACP.15: 21 residues within 4Å: Chain F: K.74, I.148, K.150, 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 Ligands: MG.16 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, 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.333, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herman, J. et al., 3-nitropyridine analogues as novel microtubule-targeting agents. Plos One (2024)

Release Date

2024-11-27

Peptides

Detyrosinated 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

Detyrosinated tubulin alpha-1B chain

Tubulin beta-2B chain

Stathmin-4

Tubulin tyrosine ligase

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