MolNFT v1 · #107959 · protein
Crystal structure of peroxidase from palm tree chamaerops excelsa
4USC: “Crystal structure of peroxidase from palm tree chamaerops excelsa”. X-ray diffraction, 7 ligands (HEM, PEO, NAG), 4 pockets (best druggability 0.80). MolNFT v1 #107959 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4USC
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxidase
- Ligands
- HEM, PEO, NAG, MAN, FUC, CA, SO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxidase | protein | 303 | 51% helix, 5% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PEO · Hydrogen peroxide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B
- CA · Calcium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.80 | 0.89 | 43 | HEM |
| 2 | 382 | 0.80 | 0.89 | 44 | HEM, PEO |
| 3 | 65 | 0.32 | 0.75 | 18 | empty |
| 4 | 58 | 0.25 | 0.72 | 12 | EDO |
Interfaces
1 interface between chains.
- A–B · 810 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 4USC · Crystal structure of peroxidase from palm tree Chamaerops excelsa · 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 4USC · PDBe 4USC
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