SMTL ID : 4ylg.1

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

Coordinates

PDB Format

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.21, A.23, A.24, G.25, K.26, T.27, S.28, D.63, N.122, K.123, D.125, L.126, C.155, A.156, T.157 Chain B: I.45, G.46, N.48 Ligands: MG.2 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.21, A:A.23, A:A.24, A:G.25, A:K.26, A:T.27, A:S.28, A:S.28, A:D.63, A:N.122, A:K.123, A:K.123, A:A.156, A:T.157, B:N.48 Water bridges: A:K.26, A:K.26, A:T.27, A:S.28, B:G.46 Salt bridges: A:K.26, A:D.125 GDP.3: 19 residues within 4Å: Chain A: I.45, G.46, N.48 Chain B: L.21, D.22, A.23, A.24, G.25, K.26, T.27, S.28, N.122, K.123, D.125, L.126, C.155, A.156, T.157 Ligands: MG.4 24 PLIP interactions: 2 interactions with chain A, 22 interactions with chain B Hydrogen bonds: A:N.48, B:L.21, B:A.23, B:A.24, B:G.25, B:K.26, B:T.27, B:S.28, B:S.28, B:D.63, B:N.122, B:K.123, B:A.156, B:T.157 Water bridges: A:F.47, B:K.26, B:K.26, B:T.27, B:S.28, B:K.123, B:K.123, B:K.123 Salt bridges: B:K.26, B:D.125

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.27, E.50 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.27, H2O.2, H2O.4, H2O.4, H2O.5 MG.4: 3 residues within 4Å: Chain B: T.27, E.50 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.27, 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

2015-05-20

Peptides

ADP-ribosylation factor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-ribosylation factor