Research workbench
Crystal structure of myeloperoxidase subform C (mpo) complex with compound-18 aka 7-(3-(2,3-dihydro-1H-inden-1-ylamino)-1- phenylpropyl)-1H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-amine
Analyse Crystal structure of myeloperoxidase subform C (mpo) complex with compound-18… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LAL
- Type
- protein
- Length
- 1,136 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, XSG, NAG, MAN, BMA, FUC, CA, CL
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 103 | 25% helix, 11% strand | P05164 |
| B | Isoform H14 of myeloperoxidase (EC 1.11.2.2) | protein | 464 | 40% helix, 9% strand | P05164 |
| D | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 104 | 25% helix, 11% strand | P05164 |
| E | Isoform H14 of myeloperoxidase (EC 1.11.2.2) | protein | 465 | 40% helix, 8% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B, D, E
- XSG · 7-[(1R)-3-{[(1R)-2,3-dihydro-1H-inden-1-yl]amino}-1-phenylpropyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine · ligand · chains D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, E, D, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, A, E, D
- 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 · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.85 | 0.92 | 57 | empty |
| 2 | 823 | 0.80 | 0.83 | 78 | HEM |
| 3 | 734 | 0.80 | 0.84 | 72 | empty |
| 4 | 725 | 0.79 | 0.83 | 54 | HEM, XSG |
| 5 | 93 | 0.66 | 0.91 | 31 | empty |
Interfaces
6 interfaces between chains.
- D–E · 5671 Ų buried · 110 hydrogen bonds · protein-protein
- A–B · 5448 Ų buried · 106 hydrogen bonds · protein-protein
- A–D · 624 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 378 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 279 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 1 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 7LAL · Crystal structure of myeloperoxidase subform C (mpo) complex with compound-18 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 7LAL · PDBe 7LAL · UniProt P05164
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