SMTL ID : 1mr3.1

Saccharomyces cerevisiae ADP-ribosylation Factor 2 (ScArf2) complexed with GDP-3'P at 1.6A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.31 Ligands: G3D.2, PDO.19 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.31, H2O.1, H2O.1, H2O.1, H2O.1

1 x G3D: GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE(Non-covalent)

G3D.2: 18 residues within 4Å: Chain A: L.25, D.26, G.27, A.28, G.29, K.30, T.31, T.32, D.67, N.126, K.127, D.129, L.130, C.159, A.160, T.161 Ligands: MG.1, EDO.8 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.27, A:A.28, A:G.29, A:K.30, A:T.31, A:T.32, A:T.32, A:D.67, A:N.126, A:K.127, A:K.127, A:A.160, A:T.161, A:T.161 Water bridges: A:K.30, A:T.31, A:T.31, A:T.32, A:D.67 Salt bridges: A:K.30, A:D.129

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: S.135, A.137 Ligands: EOH.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.135 Water bridges: A:S.135 EDO.4: 2 residues within 4Å: Chain A: P.152, W.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.153 EDO.5: 4 residues within 4Å: Chain A: D.93, N.95, K.127, L.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.93, A:N.95 Water bridges: A:D.96, A:K.127 EDO.6: 3 residues within 4Å: Chain A: N.112, E.113, D.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.112, A:D.114 EDO.7: 5 residues within 4Å: Chain A: T.48, F.51, R.75, W.78 Ligands: PDO.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.48, A:T.48, A:W.78 EDO.8: 4 residues within 4Å: Chain A: T.32, A.160, T.161 Ligands: G3D.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.160 EDO.9: 3 residues within 4Å: Chain A: R.97, A.133, E.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.97, A:E.138 Water bridges: A:S.135 EDO.10: 7 residues within 4Å: Chain A: R.19, I.20, L.21, T.64, Y.81, N.84, T.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.19, A:N.84 Water bridges: A:I.20, A:H.80 EDO.11: 3 residues within 4Å: Chain A: K.36, K.38 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.36 EDO.12: 5 residues within 4Å: Chain A: K.7, S.162, G.163, E.164 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.7, A:E.168

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain A: R.83, E.115, L.116, R.117, N.118, Q.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:N.118, A:Q.180 GOL.14: 7 residues within 4Å: Chain A: G.50, F.51, N.52, W.66, D.67 Ligands: PDO.19, PDO.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.52, A:N.52, A:D.67 Water bridges: A:G.50

4 x EOH: ETHANOL(Non-functional Binders)

EOH.15: 7 residues within 4Å: Chain A: L.25, I.92, D.93, D.96, R.99, I.100, A.103 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.92, A:D.96, A:I.100 EOH.16: 2 residues within 4Å: Chain A: S.135 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.135 Water bridges: A:S.135 EOH.17: 2 residues within 4Å: Chain A: Q.156, E.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.156, A:Q.156 EOH.18: 1 residues within 4Å: Chain A: E.164 No protein-ligand interaction detected (PLIP)

2 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.19: 8 residues within 4Å: Chain A: T.31, N.52, E.54, V.65, W.66, D.67 Ligands: MG.1, GOL.14 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.52, A:E.54 Hydrogen bonds: A:E.54, A:E.54, A:V.65, A:D.67 Water bridges: A:T.31 PDO.20: 7 residues within 4Å: Chain A: F.51, Q.71, D.72, R.73, W.78 Ligands: EDO.7, GOL.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.73 Water bridges: A:R.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amor, J.C. et al., Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases. J.Biol.Chem. (2001)

Release Date

2002-11-20

Peptides

ADP-ribosylation factor 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

ADP-ribosylation factor 2