SMTL ID : 3nkv.2 (1 other biounit)

Crystal structure of Rab1b covalently modified with AMP at Y77

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

GNP.1: 22 residues within 4Å: Chain A: D.17, S.18, G.19, V.20, G.21, K.22, S.23, C.24, Y.34, E.36, T.41, T.65, A.66, G.67, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: MG.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:S.18, A:G.19, A:V.20, A:G.21, A:K.22, A:K.22, A:S.23, A:S.23, A:C.24, A:E.36, A:G.67, A:N.122, A:K.123, A:A.153, A:K.154 Water bridges: A:S.18, A:S.23, A:T.41, A:T.41, A:T.41, A:T.41, A:D.64, A:Q.68, A:K.123, A:K.123 Salt bridges: A:E.36, A:D.125 pi-Stacking: A:Y.34, A:Y.34

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x BA: BARIUM ION(Non-covalent)

BA.3: 2 residues within 4Å: Chain A: D.133, T.135 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.133, A:T.135, H2O.1, H2O.3, H2O.5

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.4: 5 residues within 4Å: Chain A: K.11, F.46, Q.61, W.63, Y.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.11, A:Q.61 pi-Stacking: A:W.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muller, M.P. et al., The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b. Science (2010)

Release Date

2010-08-04

Peptides

Ras-related protein Rab-1B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ras-related protein Rab-1B

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