MolNFT v1 · #51272 · protein
Crystal structure of the C45S mutant of the peroxiredoxin 6 of arenicola marina. monoclinic form
2V2G: “Crystal structure of the C45S mutant of the peroxiredoxin 6 of arenicola marina. monoclinic form”. X-ray diffraction, 1 ligand (BEZ), 13 pockets (best druggability 0.81). MolNFT v1 #51272 on GenesisL1: 3D structure, binding sites…
- PDB
- 2V2G
- Type
- protein
- Length
- 877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin 6
- EC
- 1.11.1.15
- UniProt
- Q1AN22
- Ligands
- BEZ
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peroxiredoxin 6 (EC 1.11.1.15) | protein | 220 | 30% helix, 26% strand | Q1AN22 |
| B | Peroxiredoxin 6 (EC 1.11.1.15) | protein | 218 | 30% helix, 27% strand | Q1AN22 |
| D | Peroxiredoxin 6 (EC 1.11.1.15) | protein | 219 | 29% helix, 26% strand | Q1AN22 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.81 | 0.84 | 83 | empty |
| 2 | 647 | 0.80 | 0.85 | 56 | GOL |
| 3 | 75 | 0.62 | 0.91 | 19 | GOL |
| 4 | 80 | 0.60 | 0.89 | 20 | empty |
| 5 | 174 | 0.55 | 0.80 | 35 | BEZ |
Interfaces
5 interfaces between chains.
- A–B · 2373 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2360 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 320 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 208 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 197 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2V2G · Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of 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 Q1AN22
- Elsewhere: RCSB PDB 2V2G · PDBe 2V2G · UniProt Q1AN22
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