Research workbench
Crystal structure of myeloperoxidase subform C (mpo) complex with compound-14 aka 7-({1-[(3-PHENOXYPHENYL)METHYL]-1H-pyrazol-4- YL}METHYL)-3H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-amine
Analyse Crystal structure of myeloperoxidase subform C (mpo) complex with compound-14… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LAG
- Type
- protein
- Length
- 2,269 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase light chain; Isoform H14 of myeloperoxidase
- EC
- 1.11.2.2
- UniProt
- P05164
- Ligands
- HEM, XSD, NAG, MAN, BMA, FUC, CA, CL
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% 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, 11% strand | P05164 |
| B, G, I | Isoform H14 of myeloperoxidase (EC 1.11.2.2) | protein | 464 | 41% helix, 9% strand | P05164 |
| E | Isoform H14 of myeloperoxidase (EC 1.11.2.2) | protein | 465 | 41% helix, 9% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, D, E, F, G, H, I
- XSD · 7-({1-[(3-phenoxyphenyl)methyl]-1H-pyrazol-4-yl}methyl)-3H-[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 · 17 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 · 4 copies · chains A, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.81 | 0.84 | 89 | MAN |
| 2 | 837 | 0.80 | 0.83 | 87 | MAN |
| 3 | 1116 | 0.80 | 0.81 | 90 | HEM, XSD |
| 4 | 686 | 0.78 | 0.83 | 57 | HEM, XSD |
| 5 | 738 | 0.78 | 0.82 | 64 | HEM, XSD |
Interfaces
15 interfaces between chains.
- F–G · 5692 Ų buried · 112 hydrogen bonds · protein-protein
- A–B · 5685 Ų buried · 112 hydrogen bonds · protein-protein
- D–E · 5660 Ų buried · 113 hydrogen bonds · protein-protein
- H–I · 5639 Ų buried · 115 hydrogen bonds · protein-protein
- E–I · 724 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LAG · CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-14 AKA… · 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 7LAG · PDBe 7LAG · UniProt P05164
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