Research workbench
Crystal structure of myeloperoxidase subform C (mpo) complex with compound-24 aka 7-({4-chloro-3'-fluoro-[1,1'- biphenyl]-3- YL}METHOXY)-3H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN- 5-amine
Analyse Crystal structure of myeloperoxidase subform C (mpo) complex with compound-24… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QJ3
- Type
- protein
- Length
- 1,135 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
- HEM, JXP, NAG, MAN, BMA, FUC, CA, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Myeloperoxidase (EC 1.11.2.2) | protein | 103 | 25% helix, 11% strand | P05164 |
| B | Myeloperoxidase (EC 1.11.2.2) | protein | 464 | 43% helix, 9% strand | P05164 |
| E | Myeloperoxidase (EC 1.11.2.2) | protein | 465 | 42% helix, 9% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B, D, E
- JXP · 7-[(4-chloro-3'-fluoro[1,1'-biphenyl]-3-yl)methoxy]-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, E, D, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains E, D, B, A
- 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 · 2 copies · chains A, B
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 | 762 | 0.80 | 0.83 | 79 | MAN, FUC |
| 2 | 795 | 0.79 | 0.82 | 66 | HEM |
| 3 | 750 | 0.78 | 0.82 | 61 | HEM, JXP |
| 4 | 81 | 0.44 | 0.80 | 21 | empty |
| 5 | 55 | 0.38 | 0.81 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5664 Ų buried · 112 hydrogen bonds · protein-protein
- D–E · 5624 Ų buried · 112 hydrogen bonds · protein-protein
- A–D · 636 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 379 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide, 1 cofactor (N-glycosylation, disulfide, heme attachment).
Compared structures
- 5QJ3 · Crystal structure of myeloperoxidase subform C (mpo) complex with compound-24 aka… · 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 E 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 5QJ3 · PDBe 5QJ3 · UniProt P05164
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