MolNFT v1 · #131944 · protein
Crystal structure of myeloperoxidase subform C (mpo) omplex with compound-20 aka 7-((3-(1-methyl-1H-pyrazol-3- YL)BENZYL)OXY)- 1H-[1, 2,3]TRIAZOLO[4,5-B]PYRIDIN-5-amine
5QJ2: “Crystal structure of myeloperoxidase subform C (mpo) omplex with compound-20 aka…”. X-ray diffraction, 8 ligands (HEM, JXS, NAG), 17 pockets (best druggability 0.80). MolNFT v1 #131944 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5QJ2
- Type
- protein
- Length
- 2,272 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase
- EC
- 1.11.2.2
- UniProt
- P05164
- Ligands
- HEM, JXS, NAG, MAN, FUC, BMA, CA, CL
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, H | Myeloperoxidase (EC 1.11.2.2) | protein | 103 | 22% helix, 11% strand | P05164 |
| B, E, G, I | Myeloperoxidase (EC 1.11.2.2) | protein | 465 | 39% 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
- JXS · 7-{[3-(1-methyl-1H-pyrazol-3-yl)phenyl]methoxy}-1H-[1, 2,3]triazolo[4,5-b]pyridin-5-amine · ligand · 3 copies · chains A, B, D, E, F, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains B, E, D, A, 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 · 2 copies · chains B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.80 | 0.82 | 90 | HEM, JXS |
| 2 | 650 | 0.79 | 0.84 | 70 | MAN |
| 3 | 777 | 0.79 | 0.82 | 63 | HEM |
| 4 | 765 | 0.79 | 0.83 | 79 | FUC, MAN |
| 5 | 803 | 0.79 | 0.82 | 64 | HEM, JXS |
Interfaces
14 interfaces between chains.
- D–E · 5732 Ų buried · 113 hydrogen bonds · protein-protein
- F–G · 5718 Ų buried · 108 hydrogen bonds · protein-protein
- H–I · 5671 Ų buried · 113 hydrogen bonds · protein-protein
- A–B · 5593 Ų buried · 112 hydrogen bonds · protein-protein
- F–H · 681 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5QJ2 · Crystal structure of myeloperoxidase subform C (mpo) omplex with compound-20 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 B 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 5QJ2 · PDBe 5QJ2 · UniProt P05164
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