MolNFT v1 · #63437 · protein
Crystal structure of myeloperoxidase from human leukocytes
3F9P: “Crystal structure of myeloperoxidase from human leukocytes”. X-ray diffraction, 6 ligands (HEM, NAG, BMA), 13 pockets (best druggability 0.80). MolNFT v1 #63437 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3F9P
- Type
- protein
- Length
- 1,146 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase
- EC
- 1.11.1.7
- UniProt
- P05164
- Ligands
- HEM, NAG, BMA, FUC, CA, CL
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Myeloperoxidase (EC 1.11.1.7) | protein | 107 | 24% helix, 10% strand | P05164 |
| C, D | Myeloperoxidase (EC 1.11.1.7) | protein | 466 | 41% helix, 9% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, D, B, A
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains D, B, C, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C, D
- CA · Calcium ion · metal · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.80 | 0.83 | 59 | HEM |
| 2 | 667 | 0.79 | 0.84 | 63 | empty |
| 3 | 881 | 0.79 | 0.81 | 66 | HEM |
| 4 | 120 | 0.48 | 0.80 | 16 | empty |
| 5 | 82 | 0.48 | 0.82 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5886 Ų buried · 106 hydrogen bonds · protein-protein
- B–D · 5862 Ų buried · 109 hydrogen bonds · protein-protein
- A–B · 757 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 414 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 273 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide, 6 cofactor, 6 glycan, 2 modified (disulfide, heme attachment, N-glycosylation, 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 3F9P · PDBe 3F9P · UniProt P05164
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