SMTL ID : 4lhw.1 (4 other biounits)

Crystal structure of Rab8 in its active GppNHp-bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.20, T.38 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.20, A:T.38, H2O.1, H2O.1

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

GNP.2: 25 residues within 4Å: Chain A: D.14, S.15, G.16, V.17, G.18, K.19, T.20, C.21, F.31, N.32, S.33, T.34, F.35, S.37, T.38, A.63, G.64, N.119, K.120, D.122, V.123, S.149, A.150, K.151 Ligands: MG.1 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:S.15, A:G.16, A:V.17, A:G.18, A:K.19, A:K.19, A:T.20, A:T.20, A:C.21, A:T.34, A:T.38, A:T.38, A:G.64, A:N.119, A:K.120, A:A.150, A:K.151 Water bridges: A:S.15, A:S.15, A:T.20, A:S.33, A:F.35, A:I.36, A:I.36, A:Q.65, A:K.120, A:K.120 Salt bridges: A:D.122 pi-Stacking: A:F.31, A:F.31

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 4 residues within 4Å: Chain A: W.60, Y.75, G.78, A.79 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.60 Hydrogen bonds: A:K.8, A:Y.75, A:G.78 Water bridges: A:K.8, A:Q.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Z. et al., Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB. J.Biol.Chem. (2013)

Release Date

2013-10-09

Peptides

Ras-related protein Rab-8A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ras-related protein Rab-8A

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