Research workbench
Crystal structure of human myeloperoxidase at 1.7 ångströms resolution
Analyse Crystal structure of human myeloperoxidase at 1.7 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FIW
- Type
- protein
- Length
- 1,136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase
- EC
- 1.11.2.2
- UniProt
- P05164
- Ligands
- HEM, NAG, BMA, MAN, FUC, CA, CL
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloperoxidase (EC 1.11.2.2) | protein | 105 | 25% helix, 10% strand | P05164 |
| B | Myeloperoxidase (EC 1.11.2.2) | protein | 103 | 25% helix, 11% strand | P05164 |
| C, D | Myeloperoxidase (EC 1.11.2.2) | protein | 464 | 41% helix, 8% 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 · 4 copies · chains D, C, B, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains D, C
- 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 · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.80 | 0.83 | 82 | FUC, BMA |
| 2 | 866 | 0.79 | 0.82 | 66 | HEM |
| 3 | 789 | 0.78 | 0.82 | 64 | HEM |
| 4 | 78 | 0.48 | 0.82 | 20 | empty |
| 5 | 65 | 0.39 | 0.79 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5744 Ų buried · 111 hydrogen bonds · protein-protein
- B–D · 5695 Ų buried · 115 hydrogen bonds · protein-protein
- A–B · 668 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 375 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 277 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 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 5FIW · PDBe 5FIW · UniProt P05164
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