MolNFT v1 · #52925 · protein
Crystal structure of peroxiredoxin 5 from arenicola marina
2WFC: “Crystal structure of peroxiredoxin 5 from arenicola marina”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #52925 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WFC
- Type
- protein
- Length
- 636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin 5
- EC
- 1.11.1.15
- UniProt
- Q1AN23
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peroxiredoxin 5 (EC 1.11.1.15) | protein | 159 | 31% helix, 26% strand | Q1AN23 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.73 | 0.77 | 74 | empty |
| 2 | 63 | 0.33 | 0.75 | 11 | ACT |
| 3 | 60 | 0.33 | 0.76 | 12 | empty |
| 4 | 62 | 0.30 | 0.74 | 18 | empty |
| 5 | 65 | 0.28 | 0.73 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–C · 696 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 679 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 185 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 122 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WFC · Crystal structure of peroxiredoxin 5 from Arenicola Marina · 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 Q1AN23
- Elsewhere: RCSB PDB 2WFC · PDBe 2WFC · UniProt Q1AN23
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