SMTL ID : 4i1o.2 (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: 5 residues within 4Å: Chain B: S.23, T.41 Ligands: GDP.2, BEF.3, PEG.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.23, B:T.41, H2O.2

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

GDP.2: 23 residues within 4Å: Chain A: H.99, R.128 Chain B: G.19, V.20, G.21, K.22, S.23, C.24, Y.34, S.37, Y.38, I.39, T.41, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: MG.1, BEF.3, PEG.4 25 PLIP interactions: 22 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.19, B:V.20, B:G.21, B:K.22, B:S.23, B:C.24, B:S.37, B:T.41, B:T.41, B:N.122, B:K.123, B:K.123, B:S.152, B:A.153, B:K.154 Water bridges: B:T.35, B:E.36, B:T.65, A:R.128 Salt bridges: B:K.22, B:D.125, A:R.128, A:R.128 pi-Stacking: B:Y.34, B:Y.34

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

BEF.3: 10 residues within 4Å: Chain A: R.128 Chain B: S.18, G.19, K.22, S.40, T.41, A.66, G.67 Ligands: MG.1, GDP.2 No protein-ligand interaction detected (PLIP)

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

PEG.4: 7 residues within 4Å: Chain B: Y.34, T.35, E.36, Y.38, L.126, K.154 Ligands: GDP.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.34, B:E.36, B:E.36 PEG.5: 8 residues within 4Å: Chain A: N.125, K.166 Chain B: S.23, T.41, D.45, K.47, D.64 Ligands: MG.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.23, B:K.47 PEG.6: 9 residues within 4Å: Chain B: K.11, W.63, S.76, S.77, Y.78, Y.79, R.80, G.81, A.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.63, B:S.76, B:R.80, B:G.81

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

LepB

Ras-related protein Rab-1B

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