MolNFT v1 · #126850 · protein
Crystal structure of human promyeloperoxidase (prompo)
5MFA: “Crystal structure of human promyeloperoxidase (prompo)”. X-ray diffraction, 6 ligands (HEM, NAG, MAN), 4 pockets (best druggability 0.81). MolNFT v1 #126850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFA
- Type
- protein
- Length
- 588 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase
- EC
- 1.11.2.2
- UniProt
- P05164
- Ligands
- HEM, NAG, MAN, BMA, CA, CL
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloperoxidase (EC 1.11.2.2) | protein | 588 | 38% helix, 8% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 5 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.81 | 0.83 | 72 | HEM, TRS |
| 2 | 73 | 0.48 | 0.83 | 20 | empty |
| 3 | 76 | 0.41 | 0.79 | 23 | empty |
| 4 | 85 | 0.38 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 7 disulfide, 5 glycan, 3 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, oxidation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05164
- Elsewhere: RCSB PDB 5MFA · PDBe 5MFA · UniProt P05164
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