MolNFT v1 · #113742 · protein
Structure of sorghum peroxidase
5AOG · Cationic peroxidase SPC4: “Structure of sorghum peroxidase”. X-ray diffraction, 9 ligands (HEM, IAC, NAG), 1 pocket (best druggability 0.84). MolNFT v1 #113742 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5AOG
- Type
- protein
- Length
- 307 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cationic peroxidase SPC4
- EC
- 1.11.1.7
- UniProt
- P84516
- Ligands
- HEM, IAC, NAG, FUC, BMA, XYP, MAN, CA, NA
- Pockets
- 1 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cationic peroxidase SPC4 (EC 1.11.1.7) | protein | 307 | 49% helix, 5% strand | P84516 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- IAC · 1H-indol-3-ylacetic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- XYP · beta-D-xylopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.84 | 0.91 | 44 | HEM, GOL, IAC |
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P84516
- Elsewhere: RCSB PDB 5AOG · PDBe 5AOG · UniProt P84516
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