SMTL ID : 7vmk.1

Crystal structure of tubulin with 3

Coordinates

PDB Format

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: 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.143, G.144, T.145, G.146, I.171, V.177, S.178, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 25 PLIP interactions: 22 interactions with chain A, 3 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.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:T.145, A:T.145, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.13: 23 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, S.140, 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.14 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:D.98, 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:A.174 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

4 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.6: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain B: D.118 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: D.69, E.71 Ligands: GTP.13 No protein-ligand interaction detected (PLIP)

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.4: 1 residues within 4Å: Chain E: D.42 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain B: E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.15: 7 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, D.47, N.50, 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.5: 20 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, 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 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:D.177, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:G.13, B:L.139, B:G.140, B:G.141, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.16: 16 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 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 Water bridges: D:G.13

2 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 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.156 Salt bridges: B:D.197, B:R.251 MES.9: 7 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, R.306, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.295, B:S.296 Salt bridges: B:R.306

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

PEG.11: 6 residues within 4Å: Chain B: G.98, N.100, K.103, W.397 Chain C: T.253, T.257 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.100, B:K.103

1 x 7PL: N-[3-[[6-[[3-(trifluoromethyl)phenyl]amino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide(Non-covalent)

7PL.12: 21 residues within 4Å: Chain A: T.179 Chain B: N.165, E.198, Y.200, V.236, T.237, C.239, L.240, L.246, A.248, D.249, L.250, K.252, L.253, N.256, A.314, A.315, I.316, K.350, T.351, A.352 21 PLIP interactions: 20 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.240, B:L.246, B:L.250, B:L.253, B:L.253, B:N.256, B:A.314, B:I.316, B:K.350 Hydrogen bonds: B:V.236, B:D.249, B:D.249, B:D.249, B:N.256, A:T.179 Water bridges: B:N.165 Halogen bonds: B:K.350

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

ACP.17: 18 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, T.241, N.242, D.318, I.330, E.331, N.333 15 PLIP interactions: 15 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:D.200, F:R.202, 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

Jifa, Z. et al., Crystal structure of tubulin with 3. To Be Published

Release Date

2022-10-19

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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