SMTL ID : 4rke.1

Drosophila melanogaster Rab2 bound to GMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 25 residues within 4Å: Chain A: D.18, T.19, G.20, V.21, G.22, K.23, S.24, C.25, F.35, Q.36, P.37, V.38, H.39, L.41, T.42, A.67, G.68, N.123, K.124, D.126, L.127, S.153, A.154, R.155 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:T.19, A:T.19, A:G.20, A:V.21, A:G.22, A:K.23, A:K.23, A:S.24, A:S.24, A:C.25, A:Q.36, A:T.42, A:G.68, A:L.69, A:N.123, A:K.124, A:K.124, A:S.153, A:A.154, A:R.155 Water bridges: A:S.24, A:D.40, A:T.42, A:T.42 Salt bridges: A:H.39, A:D.126 pi-Stacking: A:F.35, A:F.35

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.24, T.42 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.24, A:T.42, H2O.1, H2O.1

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 6 residues within 4Å: Chain A: E.139, A.142, R.143, L.147, V.148, E.170 No protein-ligand interaction detected (PLIP) 1PE.4: 5 residues within 4Å: Chain A: R.73, R.77, T.103, W.104, D.107 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.73, A:R.73 Water bridges: A:D.18, A:D.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lardong, J.A. et al., Structures of Drosophila melanogaster Rab2 and Rab3 bound to GMPPNP. Acta Crystallogr F Struct Biol Commun (2015)

Release Date

2014-12-10

Peptides

GH01619p: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GH01619p