SMTL ID : 6tiz.1

DROSOPHILA GDP-TUBULIN Y222F MUTANT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-1-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.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 28 PLIP interactions: 23 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, 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 Water bridges: A:G.13, A:E.71, A:N.101, A:N.101, A:F.141, A:T.145, A:T.145, B:Q.245, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.11: 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.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.12 26 PLIP interactions: 3 interactions with chain D, 23 interactions with chain C Water bridges: D:K.252, D:K.252, C:S.140, C:F.141, C:T.145, C:T.145, C:A.174 Salt bridges: D:K.252 Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, C:A.99, 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.347, B:N.347 Water bridges: A:K.394, A:K.394, A:K.394 Salt bridges: A:K.394 SO4.4: 4 residues within 4Å: Chain A: R.308, R.339, T.340, I.341 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.340, A:T.340, A:T.340, A:I.341 Water bridges: A:R.308, A:R.308, A:Q.342 Salt bridges: A:R.308, A:R.339 SO4.5: 5 residues within 4Å: Chain A: N.216, V.275, L.286, A.294, N.300 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.216, A:N.300 Water bridges: A:N.216, A:V.275, A:V.275, A:N.300 SO4.9: 3 residues within 4Å: Chain B: T.221, G.223, R.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.223 Salt bridges: B:R.276 SO4.10: 5 residues within 4Å: Chain B: K.216, L.217, T.218, T.219 Chain C: K.326 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.218, B:T.218, B:T.219 Salt bridges: C:K.326 SO4.13: 4 residues within 4Å: Chain C: Y.262, I.265, D.431, V.435 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.431, C:D.431 SO4.14: 3 residues within 4Å: Chain C: P.175, K.394 Chain D: N.347 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.347 Water bridges: D:N.347 Salt bridges: C:K.394 SO4.15: 3 residues within 4Å: Chain C: D.211, R.215, K.304 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.211 Salt bridges: C:R.215, C:K.304 SO4.17: 3 residues within 4Å: Chain D: T.221, G.223, R.276 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.223 Water bridges: D:T.221, D:R.276, D:R.276, D:R.276 Salt bridges: D:R.276 SO4.18: 6 residues within 4Å: Chain D: K.19, E.22, H.227, S.230, R.276, R.359 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.22, D:S.230 Water bridges: D:K.19, D:R.276, D:R.359, D:R.359 Salt bridges: D:K.19, D:H.227, D:R.359 SO4.19: 1 residues within 4Å: Chain D: H.396 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Water bridges: E:K.138, E:K.138 Salt bridges: E:K.138, D:H.396 SO4.20: 6 residues within 4Å: Chain D: A.271, P.272, L.273, L.284, Q.292, N.298 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.273, D:N.298 SO4.21: 3 residues within 4Å: Chain E: H.113, A.116, R.120 4 PLIP interactions: 4 interactions with chain E Water bridges: E:M.117, E:M.117 Salt bridges: E:H.113, E:R.120

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.105, T.109, G.410, E.411 Chain E: R.59, Q.62, E.63 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Water bridges: E:Q.62, A:R.105 Hydrogen bonds: A:R.105 GOL.7: 4 residues within 4Å: Chain A: V.177, R.221, T.223, Y.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.221, A:R.221, A:Y.224 Water bridges: A:T.223, A:T.225

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

GDP.8: 17 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, F.222, N.226 22 PLIP interactions: 22 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:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:N.99, B:N.99, B:S.138, B:G.140, B:G.141, B:T.143, B:S.145 pi-Stacking: B:F.222, B:F.222 GDP.16: 18 residues within 4Å: Chain D: 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, F.222, N.226 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:N.99, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:V.175, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:Q.11, D:Q.11, D:S.138, D:G.140, D:G.141, D:T.143, D:S.145 pi-Stacking: D:F.222, D: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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