SMTL ID : 6s5f.1

Structure of the human RAB39B in complex with GMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x GLY: GLYCINE(Covalent)

GLY.1: 3 residues within 4Å: Chain A: W.6, L.7, S.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.7

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

GNP.2: 24 residues within 4Å: Chain A: D.17, S.18, T.19, V.20, G.21, K.22, S.23, C.24, F.34, A.35, Q.36, S.38, P.40, T.41, A.67, G.68, H.124, K.125, D.127, L.128, S.154, A.155, R.156 Ligands: MG.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.18, A:T.19, A:V.20, A:G.21, A:K.22, A:K.22, A:K.22, A:S.23, A:C.24, A:A.35, A:S.38, A:T.41, A:T.66, A:G.68, A:K.125, A:K.125, A:A.155, A:R.156 Water bridges: A:S.23, A:S.23, A:Q.69, A:Q.69 Salt bridges: A:D.127 pi-Stacking: A:F.34, A:F.34

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

EDO.3: 2 residues within 4Å: Chain A: T.182, I.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.183

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: S.23, T.41 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.23, A:T.41, H2O.1, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Structure of the human RAB39B in complex with GMPPNP. To Be Published

Release Date

2020-07-22

Peptides

Ras-related protein Rab-39B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ras-related protein Rab-39B