SMTL ID : 4rkf.1 (1 other biounit)

Drosophila melanogaster Rab3 bound to GMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

GNP.1: 25 residues within 4Å: Chain A: N.31, S.32, S.33, V.34, G.35, K.36, T.37, S.38, F.48, T.49, S.50, A.51, F.52, S.54, T.55, A.80, G.81, N.136, K.137, D.139, M.140, S.166, A.167, K.168 Ligands: MG.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:S.33, A:V.34, A:G.35, A:K.36, A:K.36, A:T.37, A:S.38, A:S.38, A:A.51, A:T.55, A:G.81, A:N.136, A:K.137, A:A.167, A:K.168 Water bridges: A:T.37, A:V.53, A:V.53, A:T.55, A:T.55, A:L.82, A:L.82, A:K.137, A:K.137, A:K.137 Salt bridges: A:D.139 pi-Stacking: A:F.48, A:F.48

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.37, T.55 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.37, A:T.55, H2O.1, H2O.1

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

1PE.3: 7 residues within 4Å: Chain A: F.52, V.53, S.54, V.56, L.82, R.84, Y.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.54, A:R.84 Water bridges: A:S.54, A:S.54 1PE.4: 7 residues within 4Å: Chain A: N.31, E.83, R.86, S.113, D.116, W.117, Q.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.83, A:R.86, A:R.86

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

Ras-related protein Rab-3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ras-related protein Rab-3

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