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Crystal structure of myeloperoxidase subform C (mpo) complex with compound-4
Analyse Crystal structure of myeloperoxidase subform C (mpo) complex with compound-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LAE
- Type
- protein
- Length
- 1,135 residues
- Chains
- 4
- 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, XRV, NAG, MAN, FUC, BMA, CA, CL
- Pockets
- 11 · 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 | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 103 | 23% helix, 11% strand | P05164 |
| B | 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 | 40% helix, 9% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B, D, E
- XRV · 7-{[1-(4-fluorophenyl)-1H-pyrazol-4-yl]methyl}-1H-[1,2, 3]triazolo[4,5-b]pyridin-5-amine · ligand · 2 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, E, D, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, A, E, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, E
- BMA · beta-D-mannopyranose · 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.81 | 0.97 | 35 | empty |
| 2 | 714 | 0.80 | 0.84 | 72 | MAN |
| 3 | 790 | 0.80 | 0.83 | 69 | HEM, XRV |
| 4 | 782 | 0.79 | 0.82 | 67 | HEM, XRV |
| 5 | 58 | 0.60 | 0.91 | 20 | empty |
Interfaces
6 interfaces between chains.
- D–E · 5608 Ų buried · 107 hydrogen bonds · protein-protein
- A–B · 5606 Ų buried · 114 hydrogen bonds · protein-protein
- A–D · 612 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 389 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 276 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 7LAE · CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-4 · 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 7LAE · PDBe 7LAE · UniProt P05164
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