MolNFT v1 · #14105 · protein
The impact of the physical and chemical enviroment on the molecular structure of coprinus cinereus peroxidase
1LYK: “The impact of the physical and chemical enviroment on the molecular structure of coprinus cinereus peroxidase”. X-ray diffraction, 6 ligands (HEM, NAG, BMA), 2 pockets (best druggability 0.80). MolNFT v1 #14105 on GenesisL1: 3D…
- PDB
- 1LYK
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxidase
- EC
- 1.11.1.7
- UniProt
- P28314
- Ligands
- HEM, NAG, BMA, MAN, CA, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxidase (EC 1.11.1.7) | protein | 336 | 44% helix, 7% strand | P28314 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains B
- CA · Calcium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.80 | 0.88 | 39 | HEM |
| 2 | 409 | 0.80 | 0.88 | 40 | HEM |
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 1LYK · The impact of the physical and chemical enviroment on the molecular structure of coprinus… · the same entry in another collection · chain A against A, TM-score 1.00
- P28314 · AlphaFold monomer V2.0 prediction for peroxidase (P28314) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P28314
- Elsewhere: RCSB PDB 1LYK · PDBe 1LYK · UniProt P28314
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