SMTL ID : 6tiy.1

DROSOPHILA GMPCPP-TUBULIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 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 29 PLIP interactions: 24 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:A.99, A:A.100, 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, A:T.145, A:A.174, A:T.179, B:Q.245, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: 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: 22 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, 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:D.98, C:S.140, C:F.141, C:T.145, C:T.145, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: G2P.7 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) MG.16: 1 residues within 4Å: Ligands: G2P.15 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:K.394, A:K.394 Salt bridges: A:K.394 Hydrogen bonds: B:N.347 SO4.4: 5 residues within 4Å: Chain A: N.216, V.275, L.286, A.294, N.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.216, A:N.300, A:N.300 Water bridges: A:V.275, A:V.275 SO4.5: 4 residues within 4Å: Chain A: R.308, R.339, T.340, I.341 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.340, A:T.340, A:T.340, A:I.341 Water bridges: A:R.308, A:Q.342 Salt bridges: A:R.308, A:R.339 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 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: 4 residues within 4Å: Chain C: Y.262, I.265, D.431, E.434 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.434 SO4.14: 3 residues within 4Å: Chain C: P.175, K.394 Chain D: N.347 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.394 Hydrogen bonds: D:N.347 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:T.221, 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 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.230 Water bridges: D:K.19, D:R.276, D:R.359 Salt bridges: D:K.19, D:H.227, D:R.359 SO4.19: 6 residues within 4Å: Chain D: A.271, P.272, L.273, L.284, Q.292, N.298 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.273, D:N.298, D:N.298 SO4.20: 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: G.410, E.411 Chain E: R.59, Q.62, E.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.105, A:E.411

2 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.7: 20 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.8 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:A.97, B:G.98, B:N.99, B:N.99, B:S.138, B:G.142, B:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 Water bridges: B:S.138, B:S.138, B:G.140, B:G.141, B:T.143, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222 G2P.15: 22 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, G.96, 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, Y.222, N.226 Ligands: MG.16 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:N.99, D:S.138, D:G.142, D:T.143, D:G.144, D:E.181, D:N.204, D:N.226, D:N.226, D:N.226 Water bridges: D:G.13, D:E.69, D:G.140, D:G.141, D:T.143, D:T.143, D:S.145, D:S.176 pi-Stacking: D:Y.222, D:Y.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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