SMTL ID : 3rwm.1

Crystal Structure of Ypt32 in Complex with GppNHp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

GNP.1: 24 residues within 4Å: Chain A: D.18, S.19, G.20, V.21, G.22, K.23, S.24, N.25, F.35, N.36, I.37, S.39, S.41, T.42, A.67, G.68, N.123, K.124, D.126, L.127, S.153, A.154, L.155 Ligands: MG.2 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:S.19, A:G.20, A:V.21, A:G.22, A:K.23, A:K.23, A:S.24, A:N.25, A:N.25, A:N.36, A:S.39, A:S.41, A:T.42, A:T.42, A:G.68, A:N.123, A:K.124, A:A.154, A:L.155 Water bridges: A:S.24, A:S.24, A:I.37, A:I.37, A:S.39, A:S.39, A:K.124, A:K.124, A:K.124 Salt bridges: A:D.126 pi-Stacking: A:F.35, A:F.35 GNP.3: 3 residues within 4Å: Chain A: G.4, D.6, K.58 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.4 Water bridges: A:D.6, A:D.6, A:D.6, A:D.6, A:K.58, A:K.58 Salt bridges: A:D.6, A:K.58

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.24, T.42, D.65 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.24, A:T.42, H2O.3, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sultana, A. et al., The activation cycle of Rab GTPase Ypt32 reveals structural determinants of effector recruitment and GDI binding. Febs Lett. (2011)

Release Date

2011-10-26

Peptides

GTP-binding protein YPT32/YPT11: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GTP-binding protein YPT32/YPT11

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