Research workbench
Crystal structure of the C45S mutant of the peroxiredoxin 6 of arenicola marina. orthorhombic form
Analyse Crystal structure of the C45S mutant of the peroxiredoxin 6 of arenicola… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V41
- Type
- protein
- Length
- 1,756 residues
- Chains
- 8
- 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
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | Peroxiredoxin 6. (EC 1.11.1.15) | protein | 220 | 30% helix, 26% strand | Q1AN22 |
| C | Peroxiredoxin 6. (EC 1.11.1.15) | protein | 216 | 31% helix, 26% strand | Q1AN22 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.79 | 0.83 | 82 | empty |
| 2 | 865 | 0.76 | 0.80 | 80 | empty |
| 3 | 893 | 0.75 | 0.79 | 52 | empty |
| 4 | 360 | 0.69 | 0.82 | 44 | empty |
| 5 | 86 | 0.68 | 0.93 | 20 | empty |
Interfaces
12 interfaces between chains.
- G–H · 2406 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2399 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2379 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2365 Ų buried · 38 hydrogen bonds · protein-protein
- C–E · 529 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2V41 · 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 2V41 · PDBe 2V41 · UniProt Q1AN22
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