SMTL ID : 4y0v.1

Structure of an ADP ribosylation factor from Entamoeba histolytica HM-1:IMSS bound to Mg-GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 19 residues within 4Å: Chain A: L.25, A.27, A.28, G.29, K.30, T.31, S.32, D.67, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Chain B: I.49, G.50, N.52 Ligands: MG.2 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.25, A:A.27, A:A.28, A:G.29, A:K.30, A:T.31, A:S.32, A:S.32, A:D.67, A:N.126, A:K.127, A:K.127, A:A.160, A:T.161, B:N.52 Water bridges: A:K.30, A:K.30, A:T.31, A:S.32, B:G.50 Salt bridges: A:K.30, A:D.129 GDP.3: 19 residues within 4Å: Chain A: I.49, G.50, N.52 Chain B: L.25, D.26, A.27, A.28, G.29, K.30, T.31, S.32, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.4 24 PLIP interactions: 22 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.25, B:A.27, B:A.28, B:G.29, B:K.30, B:T.31, B:S.32, B:S.32, B:D.67, B:N.126, B:K.127, B:A.160, B:T.161, A:N.52 Water bridges: B:K.30, B:K.30, B:T.31, B:S.32, B:K.127, B:K.127, B:K.127, A:F.51 Salt bridges: B:K.30, B:D.129

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.31, E.54 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.31, H2O.2, H2O.4, H2O.4, H2O.5 MG.4: 3 residues within 4Å: Chain B: T.31, E.54 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.31, H2O.9, H2O.10, H2O.11, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Serbzhinskiy, D.A. et al., Structure of an ADP-ribosylation factor, ARF1, from Entamoeba histolytica bound to Mg(2+)-GDP. Acta Crystallogr.,Sect.F (2015)

Release Date

2015-03-04

Peptides

ADP-ribosylation factor 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-ribosylation factor 1