SMTL ID : 4jvs.1

Crystal structure of LepB GAP domain from Legionella drancourtii in complex with Rab1-GDP and AlF3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 5 residues within 4Å: Chain A: D.226, S.227, D.232, I.233, R.265 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.232, A:I.233 Hydrogen bonds: A:D.232, A:D.232 Salt bridges: A:R.265

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

GDP.2: 22 residues within 4Å: Chain A: R.137 Chain B: S.24, G.25, V.26, G.27, K.28, S.29, C.30, Y.40, E.42, S.43, Y.44, T.47, N.128, K.129, D.131, L.132, S.158, A.159, K.160 Ligands: AF3.3, MG.4 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.23, B:G.25, B:V.26, B:G.27, B:K.28, B:S.29, B:S.29, B:C.30, B:Y.40, B:E.42, B:S.43, B:N.128, B:K.129, B:K.129, B:A.159, B:K.160 Water bridges: B:Q.74 Salt bridges: B:K.28, B:E.42, B:D.131, A:R.137, A:R.137 pi-Stacking: B:Y.40

1 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 12 residues within 4Å: Chain A: R.137 Chain B: S.24, G.25, K.28, S.29, S.46, T.47, A.72, G.73, Q.74 Ligands: GDP.2, MG.4 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain B: K.28, S.29, T.47, D.70, T.71 Ligands: GDP.2, AF3.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.29, B:T.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Q. et al., Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP. Cell Res. (2013)

Release Date

2013-05-08

Peptides

Putative uncharacterized protein: A
Ras-related protein Rab-1A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative uncharacterized protein

Ras-related protein Rab-1A