MolNFT v1 · #169010 · protein
Crystal structure of myeloperoxidase subform C (mpo) complex with compound-29 A.K.A 7-(1,2-diphenylethyl)-1H-[1,2,3]TRIAZOLO[4,5- B]PYRIDIN-5-amine
6WXZ · Myeloperoxidase light chain: “Crystal structure of myeloperoxidase subform C (mpo) complex with compound-29 A.K.A…”. X-ray diffraction, 8 ligands (HEC, UEY, NAG), 9 pockets (best druggability 0.80). MolNFT v1 #169010 on GenesisL1…
- PDB
- 6WXZ
- Type
- protein
- Length
- 1,135 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase light chain; Myeloperoxidase heavy chain
- EC
- 1.11.2.2
- UniProt
- P05164
- Ligands
- HEC, UEY, NAG, MAN, FUC, BMA, CA, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 103 | 25% helix, 11% strand | P05164 |
| B | Myeloperoxidase heavy chain (EC 1.11.2.2) | protein | 464 | 42% helix, 8% strand | P05164 |
| E | Myeloperoxidase heavy chain (EC 1.11.2.2) | protein | 465 | 41% helix, 8% strand | P05164 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B, D, E
- UEY · 7-[(1R)-1,2-diphenylethyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine · ligand · 2 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, E, A, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, D, E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, E
- BMA · beta-D-mannopyranose · 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.80 | 0.84 | 76 | MAN, FUC |
| 2 | 745 | 0.78 | 0.82 | 55 | HEC, UEY |
| 3 | 680 | 0.78 | 0.83 | 54 | HEC, UEY |
| 4 | 83 | 0.48 | 0.82 | 22 | empty |
| 5 | 64 | 0.41 | 0.81 | 20 | empty |
Interfaces
6 interfaces between chains.
- D–E · 5721 Ų buried · 104 hydrogen bonds · protein-protein
- A–B · 5678 Ų buried · 106 hydrogen bonds · protein-protein
- A–D · 630 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 384 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 278 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 cofactor, 2 modified, 1 disulfide (N-glycosylation, heme c attachment, oxidation, disulfide).
Compared structures
- 6WXZ · CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-29 A.K.A… · the same entry in another collection · chain A against A, 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 0.99
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 6WXZ · PDBe 6WXZ · UniProt P05164
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