MolNFT v1 · #148919 · protein
Crystal structure of a dye-decolorizing peroxidase from klebsiella pneumoniae (kpdyp)
6FKS · Iron-dependent peroxidase: “Crystal structure of a dye-decolorizing peroxidase from klebsiella pneumoniae (kpdyp)”. X-ray diffraction, 2 ligands (HEM, MG), 7 pockets (best druggability 0.82). MolNFT v1 #148919 on GenesisL1: 3D…
- PDB
- 6FKS
- Type
- protein
- Length
- 596 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
- 7 · best druggability 0.82
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 | 298 | 34% helix, 26% strand | A0A0W8ATM9 |
| B | Iron-dependent peroxidase (EC 1.11.1.-) | protein | 298 | 35% helix, 26% 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.82 | 0.92 | 38 | HEM |
| 2 | 352 | 0.79 | 0.89 | 41 | HEM |
| 3 | 425 | 0.70 | 0.81 | 35 | empty |
| 4 | 56 | 0.53 | 0.89 | 15 | GOL |
| 5 | 64 | 0.52 | 0.87 | 18 | GOL |
Interfaces
1 interface between chains.
- A–B · 1005 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6FKS · Crystal structure of a dye-decolorizing peroxidase from Klebsiella pneumoniae (KpDyP) · 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 6FKS · PDBe 6FKS · UniProt A0A0W8ATM9
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