SMTL ID : 8v5c.1

IpaD (122-321) Bound to Deoxycholate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: N.189, K.192 Chain B: Q.27, Y.28, K.104 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.189, A:N.189, A:K.192, B:K.104, B:K.104 GOL.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

DXC.3: 9 residues within 4Å: Chain A: I.8, L.13, K.16, S.20 Chain B: H.10, V.193, L.194, S.196, T.197 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.197, A:L.13, A:K.16 DXC.4: 8 residues within 4Å: Chain A: L.2 Chain B: W.14, I.17, I.21, V.191, L.194, S.195, T.197 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.2, B:I.17, B:I.21, B:V.191 Hydrogen bonds: B:L.194 Water bridges: B:I.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barker, S.A. et al., Structural and functional characterization of the IpaD pi-helix reveals critical roles in DOC interaction, T3SS apparatus maturation, and Shigella virulence. J.Biol.Chem. (2024)

Release Date

2024-08-21

Peptides

Invasin IpaD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Invasin IpaD