Research workbench
Crystal structure of myeloperoxidase subform C (mpo) complex with compound-40 A.K.A 7-[(1R)-1-phenyl-3-{[(1R,4R)-4- PHENYLCYCLOHEXYL]AMINO}PROPYL]-3H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5- amine
Analyse Crystal structure of myeloperoxidase subform C (mpo) complex with compound-40… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WY0
- 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, UFA, NAG, MAN, BMA, FUC, CA, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 103 | 25% helix, 11% strand | P05164 |
| B, G | Myeloperoxidase heavy chain (EC 1.11.2.2) | protein | 464 | 40% helix, 9% strand | P05164 |
| D, F | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 104 | 25% helix, 11% strand | P05164 |
| E, I | Myeloperoxidase heavy chain (EC 1.11.2.2) | protein | 465 | 39% helix, 9% strand | P05164 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, D, E, F, G, H, I
- UFA · 7-{(1R)-1-phenyl-3-[(trans-4-phenylcyclohexyl) amino]propyl}-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine · ligand · 4 copies · chains A, B, G, D, E, F, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains B, E, D, A, G, I, H, F
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains E, D, B, A, I, H, G, F
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains E, B, I, G
- FUC · alpha-L-fucopyranose · 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, D, E, F, G, 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 | 743 | 0.81 | 0.85 | 78 | empty |
| 2 | 1009 | 0.80 | 0.82 | 91 | HEC, UFA |
| 3 | 756 | 0.80 | 0.83 | 70 | MAN, FUC |
| 4 | 848 | 0.79 | 0.82 | 67 | HEC, UFA |
| 5 | 760 | 0.79 | 0.82 | 59 | HEC, UFA |
Interfaces
13 interfaces between chains.
- F–G · 5702 Ų buried · 99 hydrogen bonds · protein-protein
- A–B · 5682 Ų buried · 104 hydrogen bonds · protein-protein
- D–E · 5662 Ų buried · 105 hydrogen bonds · protein-protein
- H–I · 5654 Ų buried · 103 hydrogen bonds · protein-protein
- A–D · 691 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 12 glycan, 4 modified (heme c attachment, N-glycosylation, oxidation).
Compared structures
- 6WY0 · CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-40 A.K.A… · 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 E 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 6WY0 · PDBe 6WY0 · UniProt P05164
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