SMTL ID : 4kyi.2 (3 other biounits)

Crystal structure of the phospholipase VipD from Legionella pneumophila in complex with the human GTPase Rab5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

hetero-oligomer

Ligands

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

GNP.1: 23 residues within 4Å: Chain B: E.17, S.18, A.19, V.20, G.21, K.22, S.23, S.24, F.34, H.35, E.36, Q.38, S.40, T.41, G.67, N.122, K.123, D.125, L.126, S.152, A.153, K.154 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:S.18, B:A.19, B:V.20, B:G.21, B:K.22, B:K.22, B:S.23, B:S.24, B:H.35, B:T.41, B:T.41, B:G.67, B:N.122, B:K.123, B:K.123, B:D.125, B:A.153, B:K.154 Salt bridges: B:D.125 pi-Stacking: B:F.34, B:F.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: S.23, T.41, D.64 Ligands: GNP.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.23, B:T.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucas, M. et al., Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-08-13

Peptides

VipD: A
Ras-related protein Rab-5C: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

VipD

Ras-related protein Rab-5C

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