SMTL ID : 3hkd.1

Tubulin-TN16 : RB3 stathmin-like domain complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-2-2-1-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, I.16, D.69, E.71, D.98, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:E.71, A:D.98, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:Y.224, A:N.228, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.6: 25 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.7 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:D.98, C:S.140, C:G.144, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:Y.224, C:N.228, C:N.228, C:N.228 pi-Stacking: C:Y.224 Salt bridges: D:K.252, D:K.252

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.98, A.99, N.101, G.144, T.145 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: Q.11, N.99 Chain C: E.254 Ligands: GDP.3 No protein-ligand interaction detected (PLIP) MG.7: 8 residues within 4Å: Chain C: D.98, A.99, A.100, N.101, G.144, T.145 Chain D: K.252 Ligands: GTP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.98

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

GDP.3: 22 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, P.171, V.175, S.176, D.177, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:N.99, B:S.138, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:E.181, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.8: 19 residues within 4Å: Chain D: G.10, Q.11, C.12, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.175, S.176, D.177, E.181, N.204, Y.222, L.225, N.226 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:N.99, D:N.99, D:S.138, D:G.140, D:T.143, D:T.143, D:T.143, D:G.144, D:D.177, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222

2 x N16: (3Z,5S)-5-benzyl-3-[1-(phenylamino)ethylidene]pyrrolidine-2,4-dione(Non-covalent)

N16.5: 18 residues within 4Å: Chain A: T.179 Chain B: Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, C.239, L.240, L.246, L.250, L.253, M.257, A.314, K.350, I.368 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.167, B:Y.200, B:T.237, B:L.246, B:L.250, B:L.253, B:L.253, B:A.314, B:I.368 Hydrogen bonds: B:Y.200, B:V.236 N16.9: 17 residues within 4Å: Chain C: T.179 Chain D: Y.50, Q.134, F.167, E.198, Y.200, V.236, C.239, L.240, L.246, L.250, L.253, M.257, A.314, V.316, K.350, I.368 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.167, D:Y.200, D:V.236, D:L.240, D:L.240, D:L.246, D:L.250, D:L.253, D:L.253, D:A.314, D:I.368 Hydrogen bonds: D:Y.200, D:V.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dorleans, A. et al., Variations in the colchicine-binding domain provide insight into the structural switch of tubulin. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-09-01

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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