Research workbench
The impact of the physical and chemical environment on the molecular structure of coprinus cinereus peroxidase
Analyse The impact of the physical and chemical environment on the molecular structure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LY9
- 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, CA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxidase (EC 1.11.1.7) | protein | 336 | 43% helix, 7% strand | P28314 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.82 | 0.89 | 45 | HEM |
| 2 | 403 | 0.80 | 0.88 | 38 | HEM |
| 3 | 221 | 0.53 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 409 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1LY9 · The impact of the physical and chemical environment on the molecular structure of… · 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 1LY9 · PDBe 1LY9 · UniProt P28314
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