Research workbench
Raphanus sativus anionic peroxidase.
Analyse Raphanus sativus anionic peroxidase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A5G
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anionic peroxidase
- EC
- 1.11.1.7
- Ligands
- HEM, NAG, BMA, FUC, MAN, XYP, FUL, CA
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anionic peroxidase (EC 1.11.1.7) | protein | 307 | 49% helix, 3% strand | — |
| B | Anionic peroxidase (EC 1.11.1.7) | protein | 307 | 49% helix, 5% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- XYP · beta-D-xylopyranose · sugar · 3 copies
- FUL · beta-L-fucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 7 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains 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 | 942 | 0.79 | 0.81 | 93 | HEM |
| 2 | 343 | 0.79 | 0.89 | 43 | HEM |
Interfaces
1 interface between chains.
- A–B · 376 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 4A5G · Raphanus sativus anionic peroxidase. · 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 4A5G · PDBe 4A5G
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