SMTL ID : 4i1o.1 (3 other biounits)

Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: S.23, T.41, D.64, T.65 Ligands: GDP.2, BEF.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.23, A:T.41, A:D.64, H2O.1

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

GDP.2: 25 residues within 4Å: Chain A: S.18, G.19, V.20, G.21, K.22, S.23, C.24, Y.34, S.37, Y.38, I.39, T.41, D.64, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Chain B: H.99, R.128 Ligands: MG.1, BEF.3, PEG.4 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.19, A:V.20, A:G.21, A:K.22, A:S.23, A:C.24, A:Y.34, A:S.37, A:T.41, A:N.122, A:K.123, A:K.123, A:A.153, A:K.154, A:K.154 Water bridges: A:S.23, B:R.128, B:R.128 Salt bridges: A:K.22, A:D.125, B:R.128, B:R.128

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 9 residues within 4Å: Chain A: S.18, G.19, K.22, S.40, T.41, G.67 Chain B: R.128 Ligands: MG.1, GDP.2 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: Y.34, T.35, E.36, Y.38, L.126, K.154 Ligands: GDP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.36 PEG.5: 5 residues within 4Å: Chain B: L.246, D.283, G.286, K.287, K.290 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mihai Gazdag, E. et al., Mechanism of Rab1b deactivation by the Legionella pneumophila GAP LepB. Embo Rep. (2013)

Release Date

2013-01-16

Peptides

Ras-related protein Rab-1B: A
LepB: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Ras-related protein Rab-1B

LepB

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