MolNFT v1 · #54927 · protein
X-ray crystallographic structure of E. COLI ppix-efeb
2Y4E · Peroxidase ycdb: “X-ray crystallographic structure of E. COLI ppix-efeb”. X-ray diffraction, 2 ligands (PP9, SO4), 11 pockets (best druggability 0.83). MolNFT v1 #54927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Y4E
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxidase ycdb
- EC
- 1.11.1.-
- UniProt
- P31545
- Ligands
- PP9, SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxidase ycdb (EC 1.11.1.-) | protein | 384 | 25% helix, 23% strand | P31545 |
Ligands and binding sites
- PP9 · Protoporphyrin IX · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.83 | 0.95 | 39 | empty |
| 2 | 414 | 0.82 | 0.90 | 53 | PP9 |
| 3 | 401 | 0.81 | 0.90 | 56 | PP9 |
| 4 | 199 | 0.64 | 0.84 | 34 | empty |
| 5 | 101 | 0.56 | 0.85 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2442 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
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 P31545
- Elsewhere: RCSB PDB 2Y4E · PDBe 2Y4E · UniProt P31545
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