SMTL ID : 3cpj.1

Crystal structure of Ypt31 in complex with yeast Rab-GDI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: E.144, R.147, L.185, G.186, T.189 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: L.89, M.90, F.421, E.422 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: S.27 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.27, H2O.17, H2O.17, H2O.17, H2O.17

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

GDP.4: 19 residues within 4Å: Chain B: D.21, S.22, G.23, V.24, G.25, K.26, S.27, N.28, F.38, N.39, M.40, N.126, K.127, D.129, L.130, S.156, A.157, L.158 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:D.21, B:G.23, B:G.25, B:K.26, B:S.27, B:S.27, B:S.27, B:N.28, B:N.28, B:N.39, B:N.126, B:K.127, B:K.127, B:A.157, B:L.158 Salt bridges: B:K.26, B:D.129 pi-Stacking: B:F.38, B:F.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ignatev, A. et al., A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism. J.Biol.Chem. (2008)

Release Date

2008-05-06

Peptides

Rab GDP-dissociation inhibitor: A
GTP-binding protein YPT31/YPT8: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
B

Rab GDP-dissociation inhibitor

GTP-binding protein YPT31/YPT8

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