SMTL ID : 3x1y.1

Ras-related protein Rap1B(L9V) with GppNHp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

monomer

Ligands

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

GNP.1: 20 residues within 4Å: Chain A: G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, E.30, K.31, G.60, Q.63, N.116, K.117, D.119, L.120, S.147, A.148, K.149 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:K.16, A:S.17, A:A.18, A:E.30, A:K.31, A:G.60, A:Q.63, A:Q.63, A:N.116, A:K.117, A:K.117, A:A.148, A:K.149 Water bridges: A:S.17, A:S.17, A:S.17, A:S.17, A:Q.63 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: G.12, G.13, V.14, S.83, T.85, A.86, T.89, K.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.12, A:S.83, A:S.83

1 x CD: CADMIUM ION(Non-covalent)

CD.4: 3 residues within 4Å: Chain A: E.156, D.160, R.163 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.156, A:D.160, A:D.160, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noguchi, H. et al., The structure and conformational switching of Rap1B. Biochem.Biophys.Res.Commun. (2015)

Release Date

2015-06-03

Peptides

Ras-related protein Rap-1b: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ras-related protein Rap-1b