MolNFT v1 · #148855 · protein
Crystal structure of a dye-decolorizing peroxidase D143AR232A variant from klebsiella pneumoniae (kpdyp)
6FIY · Iron-dependent peroxidase: “Crystal structure of a dye-decolorizing peroxidase D143AR232A variant from klebsiella pneumoniae (kpdyp)”. X-ray diffraction, 2 ligands (HEM, MG), 5 pockets (best druggability 0.84). MolNFT v1 #148855 on…
- PDB
- 6FIY
- 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
- Pockets
- 5 · best druggability 0.84
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
- GOL · Glycerol · additive · 4 copies · chains A, 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 | 517 | 0.84 | 0.91 | 50 | HEM, GOL |
| 2 | 502 | 0.84 | 0.90 | 52 | HEM, GOL |
| 3 | 410 | 0.68 | 0.81 | 36 | empty |
| 4 | 193 | 0.43 | 0.73 | 29 | empty |
| 5 | 148 | 0.38 | 0.72 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1004 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6FIY · Crystal structure of a dye-decolorizing peroxidase D143AR232A variant from Klebsiella… · 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
- Every structure of UniProt A0A0W8ATM9
- Elsewhere: RCSB PDB 6FIY · PDBe 6FIY · UniProt A0A0W8ATM9
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