Research workbench
Structure of the lactoperoxidase with bound nitric oxide and nitrite in the substrate binding site at 1.98 a resolution.
Analyse Structure of the lactoperoxidase with bound nitric oxide and nitrite in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WCS
- Type
- protein
- Length
- 595 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- EC
- 1.11.1.7
- UniProt
- A0A452E9Y6
- Ligands
- OSM, HEM, NAG, NA, CA, IOD, NO3, SCN, NO, NO2
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 38% helix, 10% strand | A0A452E9Y6 |
Ligands and binding sites
- OSM · 1-(oxidosulfanyl)methanamine · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 10 copies · chains A
- NO3 · Nitrate ion · ion · 9 copies · chains A
- SCN · Thiocyanate ion · ion · 4 copies · chains A
- NO · Nitric oxide · ion · chains A
- NO2 · Nitrite ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.80 | 0.82 | 82 | NO, NO2, EDO, IOD, NA, HEM |
| 2 | 221 | 0.52 | 0.77 | 37 | empty |
| 3 | 113 | 0.46 | 0.79 | 20 | empty |
| 4 | 102 | 0.39 | 0.75 | 16 | EDO, IOD |
| 5 | 84 | 0.36 | 0.76 | 18 | OSM |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
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 A0A452E9Y6
- Elsewhere: RCSB PDB 7WCS · PDBe 7WCS · UniProt A0A452E9Y6
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