Research workbench
Crystal structure of a dye-decolorizing peroxidase D143A variant from klebsiella pneumoniae (kpdyp)
Analyse Crystal structure of a dye-decolorizing peroxidase D143A variant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FL2
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-dependent peroxidase
- EC
- 1.11.1.-
- UniProt
- A0A0W8ATM9
- Ligands
- HEM, MG, NO2
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-dependent peroxidase (EC 1.11.1.-) | protein | 299 | 34% helix, 26% strand | A0A0W8ATM9 |
| B | Iron-dependent peroxidase (EC 1.11.1.-) | protein | 303 | 34% helix, 25% strand | A0A0W8ATM9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NO2 · Nitrite ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.83 | 0.91 | 49 | HEM, NO2 |
| 2 | 419 | 0.82 | 0.90 | 54 | HEM, NO2 |
| 3 | 451 | 0.69 | 0.80 | 42 | empty |
| 4 | 194 | 0.44 | 0.73 | 28 | empty |
| 5 | 127 | 0.36 | 0.72 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1013 Ų buried · 13 hydrogen bonds · protein-protein
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 A0A0W8ATM9
- Elsewhere: RCSB PDB 6FL2 · PDBe 6FL2 · UniProt A0A0W8ATM9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.