SMTL ID : 6tiu.1

DROSOPHILA GTP-TUBULIN Y222F MUTANT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.57 Å

Oligo State

hetero-2-2-1-mer

Ligands

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 25 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, 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 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:D.98, A:A.99, 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 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.4: 23 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, D.67, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, E.181, N.204, F.222, N.226 Chain C: E.254 Ligands: MG.5, GDP.6 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.11, B:C.12, B:A.97, B:N.99, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:N.204, B:N.226, B:N.226, B:N.226, C:E.254 pi-Stacking: B:F.222, B:F.222 GTP.9: 25 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, 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 D: K.252 Ligands: MG.10 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain D Hydrogen bonds: 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 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252 GTP.11: 23 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, F.222, L.225, N.226 Ligands: MG.12 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:E.69, D:E.69, D:A.97, D:N.99, D:N.99, D:S.138, D:G.142, D:T.143, D:G.144, D:S.176, D:S.176, D:E.181, D:N.204, D:N.226, D:N.226, D:N.226 pi-Stacking: D:F.222, D:F.222

4 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.5: 3 residues within 4Å: Chain B: Q.11, T.72 Ligands: GTP.4 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain C: D.69, E.71 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain D: Q.11, T.72 Ligands: GTP.11 No protein-ligand interaction detected (PLIP)

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.347 Salt bridges: A:K.394 SO4.7: 4 residues within 4Å: Chain B: T.221, G.223, D.224, R.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.223, B:D.224 Salt bridges: B:R.276 SO4.8: 5 residues within 4Å: Chain B: K.216, L.217, T.218, T.219 Chain C: K.326 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.216, B:T.218, B:T.218, B:T.219 Salt bridges: C:K.326 SO4.13: 3 residues within 4Å: Chain D: T.221, G.223, R.276 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.223 Salt bridges: D:R.276 SO4.14: 5 residues within 4Å: Chain D: K.19, H.227, S.230, R.276, R.359 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.230 Salt bridges: D:K.19, D:H.227, D:R.359

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

GDP.6: 20 residues within 4Å: Chain B: A.9, G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, S.145, P.171, V.175, D.177, E.181, N.204, F.222, N.226 Ligands: GTP.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:S.138, B:S.138, B:G.141, B:G.142, B:T.143, B:G.144, B:S.145, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:F.222, B:F.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ayukawa, R. et al., GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation. J.Cell Biol. (2021)

Release Date

2021-01-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

Tubulin alpha-1 chain

Tubulin beta-1 chain

Stathmin-4

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