SMTL ID : 1sa1.1

Tubulin-podophyllotoxin: stathmin-like domain complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

hetero-2-2-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: N.101, G.144, T.145 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain C: N.101, G.144, T.145 Ligands: GTP.6 No protein-ligand interaction detected (PLIP)

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

GTP.2: 23 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, A.99, 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 Ligands: MG.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:N.101, A:S.140, A:T.145, A:T.145, A:V.177, A:T.179, A:E.183, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 pi-Stacking: A:Y.224 Salt bridges: B:K.252 GTP.6: 23 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, A.99, 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 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.11, C:A.12, C:S.140, C:T.145, C:T.145, C:V.177, C:T.179, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 pi-Stacking: C:Y.224

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

GDP.3: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, S.138, G.140, G.141, G.142, T.143, P.171, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, N.226 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:T.143, B:T.143, B:T.143, B:V.175, B:D.177, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 GDP.7: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, S.138, G.140, G.141, G.142, T.143, G.144, P.171, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, N.226 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:T.143, D:T.143, D:T.143, D:V.175, D:D.177, D:E.181, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 pi-Stacking: D:Y.222

2 x POD: 9-HYDROXY-5-(3,4,5-TRIMETHOXYPHENYL)-5,8,8A,9-TETRAHYDROFURO[3',4':6,7]NAPHTHO[2,3-D][1,3]DIOXOL-6(5AH)-ONE(Non-covalent)

POD.4: 17 residues within 4Å: Chain A: T.179, V.181 Chain B: V.236, C.239, L.240, A.248, K.252, L.253, N.256, M.257, V.313, A.314, A.315, V.316, N.348, K.350, A.352 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.253, B:N.256, B:A.314, B:K.350 Hydrogen bonds: B:K.350 POD.8: 17 residues within 4Å: Chain C: T.179, V.181 Chain D: V.236, C.239, L.240, A.248, K.252, L.253, N.256, M.257, V.313, A.314, A.315, V.316, N.348, K.350, A.352 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.253, D:N.256, D:A.314, D:K.350 Hydrogen bonds: D:K.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ravelli, R.B. et al., Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain. Nature (2004)

Release Date

2004-03-23

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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