MolNFT v1 · #154794 · protein
Crystal structure of hydrogen peroxide bound bovine lactoperoxidase at 2.3 a resolution
6KMK: “Crystal structure of hydrogen peroxide bound bovine lactoperoxidase at 2.3 a resolution”. X-ray diffraction, 5 ligands (PEO, HEM, NAG), 6 pockets (best druggability 0.81). MolNFT v1 #154794 on GenesisL1: 3D structure, binding sites…
- PDB
- 6KMK
- 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
- PEO, HEM, NAG, CA, IOD
- Pockets
- 6 · best druggability 0.81
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
- PEO · Hydrogen peroxide · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · 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 · 15 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 | 1175 | 0.81 | 0.82 | 101 | HEM, IOD, PEO |
| 2 | 105 | 0.46 | 0.79 | 24 | empty |
| 3 | 165 | 0.44 | 0.75 | 24 | empty |
| 4 | 93 | 0.39 | 0.76 | 16 | IOD |
| 5 | 65 | 0.33 | 0.76 | 17 | IOD |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 6KMK · Crystal structure of hydrogen peroxide bound bovine lactoperoxidase at 2.3 A resolution · 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 6KMK · PDBe 6KMK · UniProt P80025
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