Research workbench
Crystal structure and biochemical features of dye-decolorizing peroxidase yfex from escherichia COLI O157
Analyse Crystal structure and biochemical features of dye-decolorizing peroxidase yfex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GT2
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable DEFERROCHELATASE/PEROXIDASE yfex
- EC
- 1.11.1.-
- UniProt
- P76536
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable DEFERROCHELATASE/PEROXIDASE yfex (EC 1.11.1.-) | protein | 296 | 30% helix, 26% strand | P76536 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.81 | 0.91 | 38 | HEM |
| 2 | 322 | 0.80 | 0.90 | 39 | HEM |
| 3 | 314 | 0.80 | 0.91 | 39 | HEM |
| 4 | 311 | 0.80 | 0.90 | 38 | HEM |
| 5 | 452 | 0.73 | 0.83 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1111 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1067 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 373 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 323 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 35 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5GT2 · Crystal Structure and Biochemical Features of dye-decolorizing peroxidase YfeX from… · the same entry in another collection · chain A against A, TM-score 1.00
- P76536 · AlphaFold monomer V2.0 prediction for dye-decolorizing peroxidase yfex (P76536) · 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 P76536
- Elsewhere: RCSB PDB 5GT2 · PDBe 5GT2 · UniProt P76536
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