MolNFT v1 · #169024 · protein
Crystal structure of myeloperoxidase subform C (mpo) complex with compound-12 (aka; 7-benzyl-1H-[1,2,3]TRIAZOLO[4,5-B]PYRID
6WYD · Myeloperoxidase light chain: “Crystal structure of myeloperoxidase subform C (mpo) complex with compound-12 (aka…”. X-ray diffraction, 8 ligands (HEC, 7GD, NAG), 20 pockets (best druggability 0.81). MolNFT v1 #169024 on GenesisL1…
- PDB
- 6WYD
- Type
- protein
- Length
- 2,272 residues
- Chains
- 8
- 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, 7GD, NAG, MAN, FUC, BMA, CA, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, H | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 103 | 25% helix, 13% strand | P05164 |
| B, E, G, I | Myeloperoxidase heavy chain (EC 1.11.2.2) | protein | 465 | 39% helix, 8% strand | P05164 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, D, E, F, G, H, I
- 7GD · 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine · ligand · 4 copies · chains A, B, D, E, F, G, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains B, E, A, D, G, I, F, H
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains B, A, E, D, G, F, I, H
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, E, G, I
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, E, G, I
- CA · Calcium ion · metal · 4 copies · chains A, B, D, E, F, G, H, I
- CL · Chloride ion · ion · 8 copies · chains A, B, E, D, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.81 | 0.82 | 74 | HEC, 7GD |
| 2 | 742 | 0.80 | 0.83 | 74 | MAN, FUC |
| 3 | 706 | 0.79 | 0.83 | 64 | 7GD, HEC |
| 4 | 678 | 0.78 | 0.83 | 80 | empty |
| 5 | 657 | 0.78 | 0.83 | 54 | HEC, 7GD |
Interfaces
15 interfaces between chains.
- F–G · 5705 Ų buried · 107 hydrogen bonds · protein-protein
- D–E · 5704 Ų buried · 115 hydrogen bonds · protein-protein
- A–B · 5678 Ų buried · 114 hydrogen bonds · protein-protein
- H–I · 5673 Ų buried · 109 hydrogen bonds · protein-protein
- B–G · 746 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6WYD · CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA… · the same entry in another collection · chain I against I, TM-score 1.00
- P05164 · AlphaFold monomer V2.0 prediction for myeloperoxidase (P05164) · a predicted model of the same protein · chain A 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 6WYD · PDBe 6WYD · UniProt P05164
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