SMTL ID : 7vmg.1

Crystal structure of tubulin with 17j

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 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.142, G.143, G.144, T.145, G.146, I.171, V.177, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 29 PLIP interactions: 25 interactions with chain A, 4 interactions with chain B Hydrogen bonds: 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.143, 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:Q.11, A:Q.11, A:T.145, A:T.145, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.10: 24 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, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.11 29 PLIP interactions: 25 interactions with chain C, 4 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:E.71, C:F.141, C:T.145, C:T.145, C:E.183, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

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.6: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: D.69, E.71 Ligands: GTP.10 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, G.45, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:T.41, 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 CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: Y.161, G.162, K.163 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain D: R.251 Ligand excluded by PLIP

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

GDP.5: 19 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, L.207, Y.222, N.226 Ligands: MG.6 17 PLIP interactions: 17 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:D.177, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:E.69, B:A.97 pi-Stacking: B:Y.222, B:Y.222 GDP.13: 16 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, S.176, E.181, N.204, Y.222, L.225, N.226 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, 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:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

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

MES.7: 10 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, 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 MES.8: 8 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, R.306, N.337, Y.340, F.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.296 Salt bridges: B:R.306

2 x 7PB: N-[3-[[6-[(3-methoxyphenyl)amino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide(Non-covalent)

7PB.9: 22 residues within 4Å: Chain A: T.179, V.181 Chain B: N.165, E.198, Y.200, V.236, T.237, L.240, L.246, A.248, D.249, L.250, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.348, K.350 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.200, B:V.236, B:T.237, B:L.240, B:L.250, B:L.253, B:L.253, B:N.256, B:A.314, B:I.316, B:K.350, B:K.350 Hydrogen bonds: B:V.236, B:D.249, B:D.249, B:L.253, A:T.179 Water bridges: B:N.165 7PB.14: 21 residues within 4Å: Chain C: T.179, V.181 Chain D: N.165, E.198, Y.200, V.236, T.237, L.240, L.246, A.248, D.249, L.250, K.252, L.253, N.256, M.257, T.312, V.313, A.314, N.348, K.350 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.200, D:V.236, D:T.237, D:L.240, D:L.240, D:L.246, D:A.248, D:L.250, D:L.253, D:L.253, D:L.253, D:N.256, D:A.314, D:K.350, D:K.350 Hydrogen bonds: D:V.236, D:D.249, D:D.249, C:T.179, C:T.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jifa, Z. et al., Crystal structure of tubulin with 17a. To Be Published

Release Date

2022-10-19

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B chain: BD
Stathmin-4: E
TTL: 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

TTL

Related Entries With Identical Sequence