› 4dl1

X-ray diffraction
2Å resolution

Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog

Released:
DOI: 10.2210/pdb4dl1/pdb
PDB entry 4dl1 coloured by chain, front view.
PDB entry 4dl1 coloured by chain, side view.
PDB entry 4dl1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Deconstruction of activity-dependent covalent modification of heme in human neutrophil myeloperoxidase by multistage mass spectrometry (MS(4)).
Geoghegan KF, Varghese AH, Feng X, Bessire AJ, Conboy JJ, Ruggeri RB, Ahn K, Spath SN, Filippov SV, Conrad SJ, Carpino PA, Guimarães CR, Vajdos FF
Biochemistry 51 2065-77 (2012)
PMID: 22352991

Function and Biology Details

Reaction catalysed: 
Cl(-) + H(2)O(2) + H(+) = HClO + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138570 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Myeloperoxidase light chain Chains: A, B, E, F, I, J, M, N
Molecule details ›
Chains: A, B, E, F, I, J, M, N
Length: 104 amino acids
Theoretical weight: 11.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P05164 (Residues: 167-270; Coverage: 15%)
Gene name: MPO
Myeloperoxidase heavy chain Chains: C, D, G, H, K, L, O, P
Molecule details ›
Chains: C, D, G, H, K, L, O, P
Length: 466 amino acids
Theoretical weight: 53.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P05164 (Residues: 279-744; Coverage: 67%)
Gene name: MPO
Sequence domains: Animal haem peroxidase
Structure domains: Haem peroxidase domain superfamily, animal type

Ligands and Environments


Cofactor: Ligand HEM 8 x HEM
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand CL 8 x CL
Ligand 0KY 8 x 0KY
Ligand NAG 15 x NAG
Ligand CA 8 x CA
1 modified residue:
Ligand CSO 8 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21
Unit cell:
a: 63.829Å b: 242.636Å c: 151.505Å
α: 90° β: 91.19° γ: 90°
R-values:
R R work R free
0.193 0.19 0.246

Quick links

Citations

7 citation in other articles

Cardiac phosphoproteomics during remote ischemic preconditioning: a role for the sarcomeric Z-disk proteins.
Abdul-Ghani et al. (2014)
6 more