MolNFT v1 · #103682 · protein
Crystal structure of the complex of lactoperoxidase with bromo methane at 2.41 ångström resolution
4PNX: “Crystal structure of the complex of lactoperoxidase with bromo methane at 2.41 ångström resolution”. X-ray diffraction, 5 ligands (HEM, BMM, NAG), 8 pockets (best druggability 0.80). MolNFT v1 #103682 on GenesisL1: 3D structure…
- PDB
- 4PNX
- 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, BMM, NAG, CA, IOD
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 36% helix, 9% strand | P80025 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- BMM · Bromomethane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 13 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.80 | 0.81 | 97 | HEM, BMM, IOD |
| 2 | 254 | 0.56 | 0.78 | 33 | empty |
| 3 | 108 | 0.49 | 0.80 | 23 | empty |
| 4 | 161 | 0.46 | 0.76 | 38 | IOD |
| 5 | 71 | 0.39 | 0.79 | 15 | empty |
Modifications
Observed in the structure: 7 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 4PNX · Crystal structure of the complex of lactoperoxidase with bromo methane at 2.41 angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 4PNX · PDBe 4PNX · UniProt P80025
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