SMTL ID : 3ryc.1

Tubulin: RB3 stathmin-like domain complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-1-mer

Ligands

3 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 26 PLIP interactions: 21 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:N.101, A:F.141, A:T.145, A:T.145, 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.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.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.11 25 PLIP interactions: 22 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, 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 Water bridges: C:G.13, C:E.71, C:D.98, 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 GTP.14: 21 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.15 24 PLIP interactions: 24 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: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:N.99, D:L.139, D:T.143, D:S.145, D:S.145, D:S.176 pi-Stacking: D:Y.222, D:Y.222

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

MG.2: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.10 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: Q.11 Ligands: GTP.14 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 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: 5 residues within 4Å: Chain A: N.216, V.275, L.286, A.294, N.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.216, A:V.275, A:N.300 Water bridges: A:N.300 SO4.5: 3 residues within 4Å: Chain A: R.308, R.339, S.340 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.340 Water bridges: A:I.341, A:I.341, A:Q.342 Salt bridges: A:R.308, A:R.339 SO4.6: 5 residues within 4Å: Chain A: V.177, R.221, P.222, T.223, Y.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.222, A:Y.224 Water bridges: A:Y.224 Salt bridges: A:R.221 SO4.8: 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 SO4.9: 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 SO4.12: 3 residues within 4Å: Chain C: P.175, K.394 Chain D: N.347 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.347, D:N.347 Water bridges: C:K.394, C:K.394 Salt bridges: C:K.394 SO4.13: 3 residues within 4Å: Chain C: Y.262, D.431, V.435 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.264, C:D.431 SO4.16: 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:Y.222, D:R.276, D:R.276, D:R.276 Salt bridges: D:R.276 SO4.17: 4 residues within 4Å: Chain D: K.19, H.227, R.276, G.277 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.277 Water bridges: D:H.227, D:S.230, D:R.276 Salt bridges: D:K.19, D:H.227 SO4.18: 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:R.120 Salt bridges: E:H.113, E:R.120

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

GDP.7: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 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:V.175, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 Water bridges: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nawrotek, A. et al., The Determinants That Govern Microtubule Assembly from the Atomic Structure of GTP-Tubulin. J.Mol.Biol. (2011)

Release Date

2011-10-05

Peptides

Tubulin alpha chain: AC
Tubulin beta 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 chain

Tubulin beta chain

Stathmin-4

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