SMTL ID : 3r9v.3 (2 other biounits)

Cocrystal Structure of Proteolytically Truncated Form of IpaD from Shigella flexneri Bound to Deoxycholate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: S.137, G.140, W.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.137, A:G.140, A:G.140 GOL.2: 4 residues within 4Å: Chain A: N.244, F.247, S.248, D.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.248, A:D.251 Water bridges: A:K.255 GOL.3: 2 residues within 4Å: Chain A: E.250, T.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.250 Water bridges: A:N.219, A:E.250

2 x DXC: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID(Non-covalent)

DXC.4: 8 residues within 4Å: Chain A: I.93, L.98, S.105, L.279 Chain B: H.95, V.278, S.281 Ligands: DXC.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.278, A:L.279 Water bridges: A:D.108 DXC.5: 8 residues within 4Å: Chain A: L.87 Chain B: W.99, I.102, I.106, V.276, L.279, S.280 Ligands: DXC.4 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.99, B:I.102, B:I.106, B:V.276, A:L.87 Hydrogen bonds: B:L.279, B:S.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barta, M.L. et al., Identification of the bile salt binding site on IpaD from Shigella flexneri and the influence of ligand binding on IpaD structure. Proteins (2012)

Release Date

2011-12-07

Peptides

Invasin ipaD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Invasin ipaD

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