Research workbench
Crystal structure of myeloperoxidase subform C (mpo) complex with compound-6 aka 7-(benzyloxy)-1H-[1,2, 3]TRIAZOLO[4,5-D]PYRIMIDIN-5- amine
Analyse Crystal structure of myeloperoxidase subform C (mpo) complex with compound-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WDJ
- Type
- protein
- Length
- 1,138 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
- AEY, HEM, NAG, MAN, BMA, FUC, CA, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloperoxidase (EC 1.11.2.2) | protein | 104 | 25% helix, 11% strand | P05164 |
| B | Myeloperoxidase (EC 1.11.2.2) | protein | 466 | 41% helix, 9% strand | P05164 |
| D | Myeloperoxidase (EC 1.11.2.2) | protein | 103 | 25% helix, 11% strand | P05164 |
| E | Myeloperoxidase (EC 1.11.2.2) | protein | 465 | 41% helix, 9% strand | P05164 |
Ligands and binding sites
- AEY · 7-(benzyloxy)-1H-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine · ligand · 2 copies · chains A, B, D, E
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, D, E, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains E, B, A, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains E, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, E
- CA · Calcium ion · metal · 2 copies · chains A, B, D, E
- CL · Chloride ion · ion · 4 copies · chains A, B, D, E
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 | 764 | 0.79 | 0.83 | 74 | MAN, FUC |
| 2 | 775 | 0.79 | 0.82 | 61 | AEY, HEM |
| 3 | 776 | 0.78 | 0.82 | 62 | HEM, AEY |
| 4 | 85 | 0.47 | 0.81 | 21 | empty |
| 5 | 74 | 0.46 | 0.82 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5682 Ų buried · 110 hydrogen bonds · protein-protein
- D–E · 5630 Ų buried · 110 hydrogen bonds · protein-protein
- A–D · 615 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 383 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 273 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 6 cofactor, 6 glycan, 2 modified (disulfide, heme attachment, N-glycosylation, oxidation).
Compared structures
- 5WDJ · Crystal structure of myeloperoxidase subform C (mpo) complex with compound-6 aka… · the same entry in another collection · chain E against E, TM-score 1.00
- P05164 · AlphaFold monomer V2.0 prediction for myeloperoxidase (P05164) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 5WDJ · PDBe 5WDJ · UniProt P05164
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