MolNFT v1 · #189494 · protein
Structure of the complex of lactoperoxidase with nitric oxide catalytic product nitrite at 1.89 a resolution.
7VIN: “Structure of the complex of lactoperoxidase with nitric oxide catalytic product nitrite at 1.89 a resolution.”. X-ray diffraction, 7 ligands (HEM, NAG, CA), 6 pockets (best druggability 0.82). MolNFT v1 #189494 on GenesisL1: 3D…
- PDB
- 7VIN
- 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
- P80025
- Ligands
- HEM, NAG, CA, ZN, IOD, SCN, NO2
- Pockets
- 6 · best druggability 0.82
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 | P80025 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- CA · Calcium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- IOD · Iodide ion · ion · 22 copies · chains A
- SCN · Thiocyanate ion · ion · 3 copies · chains A
- NO2 · Nitrite ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.82 | 0.83 | 124 | SCN, NO2, HEM, IOD |
| 2 | 124 | 0.48 | 0.79 | 24 | empty |
| 3 | 94 | 0.38 | 0.76 | 16 | IOD |
| 4 | 74 | 0.35 | 0.76 | 18 | IOD |
| 5 | 83 | 0.33 | 0.74 | 24 | EDO, SCN |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- P80025 · AlphaFold monomer V2.0 prediction for lactoperoxidase (P80025) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P80025
- Elsewhere: RCSB PDB 7VIN · PDBe 7VIN · UniProt P80025
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