SMTL ID : 6dqq.1

Crystal structure of Haemophilus influenzae OppA complex with endogenous peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ALA- ALA- ALA- ALA: ALA-ALA-ALA-ALA(Non-covalent)

ALA-ALA-ALA-ALA.1: 15 residues within 4Å: Chain A: E.32, G.33, V.34, P.35, Y.110, Y.247, N.368, H.373, W.401, R.417, G.419, W.420, H.421, D.423, Y.489 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.35, A:W.401 Hydrogen bonds: A:E.32, A:V.34, A:Y.247, A:N.368, A:R.417, A:R.417, A:G.419, A:H.421, A:D.423 Water bridges: A:G.419, A:G.419

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 2 residues within 4Å: Chain A: K.348, E.352 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.348 ACT.3: 3 residues within 4Å: Chain A: E.65, H.76, K.140 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.140 Hydrogen bonds: A:E.65 Water bridges: A:T.74 Salt bridges: A:H.76, A:K.140 ACT.4: 3 residues within 4Å: Chain A: E.324, E.325, H.327 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.324 Hydrogen bonds: A:E.325 Water bridges: A:I.323 Salt bridges: A:H.327

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: K.182, K.183 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.183 Water bridges: A:K.183, A:E.184, A:E.184 Salt bridges: A:K.182, A:K.183 SO4.6: 1 residues within 4Å: Chain A: K.193 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, K.J. et al., Oligopeptide-binding protein from nontypeableHaemophilus influenzaehas ligand-specific sites to accommodate peptides and heme in the binding pocket. J. Biol. Chem. (2019)

Release Date

2018-11-28

Peptides

Periplasmic oligopeptide-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Periplasmic oligopeptide-binding protein