SMTL ID : 2gf9.1

Crystal structure of human RAB3D in complex with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.36 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.36, H2O.1, H2O.2, H2O.3, H2O.3

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 2 residues within 4Å: Chain A: Y.21, C.184 No protein-ligand interaction detected (PLIP) UNX.3: 2 residues within 4Å: Chain A: S.46, F.47 No protein-ligand interaction detected (PLIP)

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

GDP.4: 17 residues within 4Å: Chain A: N.30, S.31, S.32, V.33, G.34, K.35, T.36, S.37, F.47, N.135, K.136, D.138, L.139, S.165, A.166, K.167 Ligands: MG.1 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:N.30, A:S.32, A:V.33, A:G.34, A:K.35, A:T.36, A:S.37, A:S.37, A:T.48, A:N.135, A:K.136, A:K.136, A:S.165, A:A.166, A:K.167 Water bridges: A:T.36, A:T.54, A:T.54, A:A.79 Salt bridges: A:K.35, A:D.138 pi-Stacking: A:F.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, B. et al., Crystal structure of human RAB3D in complex with GDP. To be Published

Release Date

2006-05-02

Peptides

Ras-related protein Rab-3D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ras-related protein Rab-3D