› 5ee4

X-ray diffraction
2.3Å resolution

The crystal structure of HpuA from Kingella denitrificans in complex with human haemoglobin

Released:
DOI: 10.2210/pdb5ee4/pdb
PDB entry 5ee4 coloured by chain, front view.
PDB entry 5ee4 coloured by chain, side view.
PDB entry 5ee4 coloured by chain, top view.
Source organisms:
Primary publication:
Structural analysis of haemoglobin binding by HpuA from the Neisseriaceae family.
Wong CT, Xu Y, Gupta A, Garnett JA, Matthews SJ, Hare SA
Nat Commun 6 10172 (2015)
PMID: 26671256

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-123239 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Transferrin-binding protein B C-lobe/N-lobe beta barrel domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 322 amino acids
Theoretical weight: 33.8 KDa
Source organism: Kingella denitrificans ATCC 33394
Expression system: Escherichia coli
UniProt:
  • Canonical: F0EX68 (Residues: 21-340; Coverage: 100%)
Gene name: HMPREF9098_0447
Sequence domains: Haemoglobin-haptoglobin utilisation, porphyrin transporter
Hemoglobin subunit alpha Chains: C, E
Molecule details ›
Chains: C, E
Length: 141 amino acids
Theoretical weight: 15.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P69905 (Residues: 2-142; Coverage: 99%)
Gene names: HBA1, HBA2
Sequence domains: Globin
Structure domains: Globins
Hemoglobin subunit beta Chains: D, F
Molecule details ›
Chains: D, F
Length: 146 amino acids
Theoretical weight: 15.89 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P68871 (Residues: 2-147; Coverage: 99%)
Gene name: HBB
Sequence domains: Globin
Structure domains: Globins

Ligands and Environments

3 bound ligands:
Ligand GOL 2 x GOL
Ligand HEM 4 x HEM
Ligand OXY 4 x OXY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 54.79Å b: 87.21Å c: 124.32Å
α: 90° β: 98.13° γ: 90°
R-values:
R R work R free
0.204 0.202 0.244
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Heme Synthesis and Acquisition in Bacterial Pathogens.
Choby et al. (2016)
4 more

3 mentions without citation

The surface lipoproteins of gram-negative bacteria: Protectors and foragers in harsh environments.
Cole et al. (2021)
2 more