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MolNFT v1 · #14097 · protein

The impact of the physical and chemical enviroment on the molecular structure of coprinus cinereus peroxidase

1LYC: “The impact of the physical and chemical enviroment on the molecular structure of coprinus cinereus peroxidase”. X-ray diffraction, 2 ligands (HEM, CA), 2 pockets (best druggability 0.80). MolNFT v1 #14097 on GenesisL1: 3D structure…

PDB
1LYC
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
2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 7% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BPeroxidase (EC 1.11.1.7)protein33643% helix, 7% strandP28314

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

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
17400.800.8475HEM
24040.790.8838HEM

Interfaces

1 interface between chains.

  • A–B · 357 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

  • 1LYC · The impact of the physical and chemical enviroment on the molecular structure of Coprinus… · 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

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