MolNFT v1 · #184226 · protein
Glycosylation in the crystal structure of neutrophil myeloperoxidase
7OIH: “Glycosylation in the crystal structure of neutrophil myeloperoxidase”. X-ray diffraction, 10 ligands (HEM, 8PR, NAG), 20 pockets (best druggability 0.82). MolNFT v1 #184226 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7OIH
- Type
- protein
- Length
- 4,567 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase
- EC
- 1.11.2.2
- UniProt
- P05164
- Ligands
- HEM, 8PR, NAG, MAN, BMA, FUC, CA, CL, PO4, SCN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloperoxidase (EC 1.11.2.2) | protein | 573 | 37% helix, 9% strand | P05164 |
| B | Myeloperoxidase (EC 1.11.2.2) | protein | 570 | 37% helix, 9% strand | P05164 |
| C | Myeloperoxidase (EC 1.11.2.2) | protein | 570 | 38% helix, 9% strand | P05164 |
| D, H | Myeloperoxidase (EC 1.11.2.2) | protein | 571 | 38% helix, 9% strand | P05164 |
| E | Myeloperoxidase (EC 1.11.2.2) | protein | 572 | 37% helix, 9% strand | P05164 |
| F | Myeloperoxidase (EC 1.11.2.2) | protein | 571 | 37% helix, 9% strand | P05164 |
| G | Myeloperoxidase (EC 1.11.2.2) | protein | 569 | 37% helix, 9% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 8PR · Paroxetine · ligand · 4 copies · chains A, D, F, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 58 copies · chains B, D, G, H, A, C, E, F
- MAN · alpha-D-mannopyranose · sugar · 28 copies · chains H, G, B, A, D, C, F, E
- BMA · beta-D-mannopyranose · sugar · 19 copies · chains H, G, A, B, D, C, E, F
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains G, H, A, B, C, D, E, F
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 36 copies · chains A, B, F, C, D, E, G, H
- PO4 · Phosphate ion · ion · 14 copies · chains A, B, F, C, D, E, G, H
- SCN · Thiocyanate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.82 | 0.85 | 68 | HEM, SCN |
| 2 | 983 | 0.82 | 0.83 | 90 | HEM, SCN, CL, PO4 |
| 3 | 784 | 0.80 | 0.84 | 82 | empty |
| 4 | 696 | 0.80 | 0.84 | 69 | MAN, FUC, CL |
| 5 | 778 | 0.80 | 0.83 | 60 | HEM, SCN, 8PR |
Interfaces
17 interfaces between chains.
- A–B · 1442 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1394 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1319 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1282 Ų buried · 14 hydrogen bonds · protein-protein
- C–H · 826 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 disulfide, 29 glycan, 16 cofactor, 8 modified (disulfide, N-glycosylation, heme attachment, oxidation).
Compared structures
- 7OIH · Glycosylation in the crystal structure of neutrophil myeloperoxidase · the same entry in another collection · chain A against A, TM-score 1.00
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 7OIH · PDBe 7OIH · UniProt P05164
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.