MolNFT v1 · #46563 · protein
Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide at 2.8 a resolution
2O86: “Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide at 2.8 a resolution”. X-ray diffraction, 7 ligands (HEM, NAG, MAN), 6 pockets (best druggability 0.81). MolNFT v1 #46563 on GenesisL1: 3D…
- PDB
- 2O86
- 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
- Ligands
- HEM, NAG, MAN, CA, IOD, NO3, CO3
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 37% helix, 9% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 7 copies · chains A
- NO3 · Nitrate ion · ion · 7 copies · chains A
- CO3 · Carbonate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.81 | 0.82 | 98 | IOD, HEM |
| 2 | 259 | 0.57 | 0.78 | 37 | empty |
| 3 | 98 | 0.52 | 0.83 | 20 | empty |
| 4 | 50 | 0.37 | 0.80 | 16 | empty |
| 5 | 89 | 0.35 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 2O86 · Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide… · 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
- Elsewhere: RCSB PDB 2O86 · PDBe 2O86
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