SMTL ID : 4f61.1

Tubulin:Stathmin-like domain complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.17 Å

Oligo State

hetero-4-4-1-mer

Ligands

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

GTP.1: 27 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, P.173, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 21 PLIP interactions: 19 interactions with chain A, 2 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:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.4: 27 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, P.173, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.5 21 PLIP interactions: 19 interactions with chain C, 2 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:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252 GTP.7: 27 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, P.173, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain F: K.252 Ligands: MG.8 21 PLIP interactions: 19 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.11, E:A.12, E:A.99, E:A.100, E:N.101, E:S.140, E:G.144, E:T.145, E:T.145, E:G.146, E:V.177, E:E.183, E:N.206, E:N.206, E:Y.224, E:N.228, E:N.228 pi-Stacking: E:Y.224, E:Y.224 Salt bridges: F:K.252, F:K.252 GTP.10: 27 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, P.173, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain H: K.252 Ligands: MG.11 21 PLIP interactions: 19 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:Q.11, G:A.12, G:A.99, G:A.100, G:N.101, G:S.140, G:G.144, G:T.145, G:T.145, G:G.146, G:V.177, G:E.183, G:N.206, G:N.206, G:Y.224, G:N.228, G:N.228 pi-Stacking: G:Y.224, G:Y.224 Salt bridges: H:K.252, H:K.252

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.71, A:E.71 MG.5: 3 residues within 4Å: Chain C: E.71 Chain D: K.252 Ligands: GTP.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.71, C:E.71 MG.8: 3 residues within 4Å: Chain E: E.71 Chain F: K.252 Ligands: GTP.7 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.71, E:E.71 MG.11: 3 residues within 4Å: Chain G: E.71 Chain H: K.252 Ligands: GTP.10 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.71, G:E.71

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

GDP.3: 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 17 PLIP interactions: 17 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:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:Y.222, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.6: 19 residues within 4Å: Chain D: 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 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:V.175, D:E.181, D:N.204, D:Y.222, D:N.226, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222 GDP.9: 19 residues within 4Å: Chain F: 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 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:S.138, F:G.142, F:T.143, F:T.143, F:T.143, F:G.144, F:V.175, F:E.181, F:N.204, F:Y.222, F:N.226, F:N.226, F:N.226 pi-Stacking: F:Y.222, F:Y.222 GDP.12: 17 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, S.176, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:S.138, H:G.142, H:T.143, H:T.143, H:T.143, H:G.144, H:S.176, H:E.181, H:N.204, H:Y.222, H:N.226, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mignot, I. et al., Design and characterization of modular scaffolds for tubulin assembly. J.Biol.Chem. (2012)

Release Date

2012-07-18

Peptides

Tubulin alpha chain: ACEG
Tubulin beta chain: BDFH
Stathmin-like domain R4: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

I
I

Tubulin alpha chain

Tubulin beta chain

Stathmin-like domain R4

Related Entries With Identical Sequence