Research workbench
Human peroxiredoxin 5 with a fragment
Analyse Human peroxiredoxin 5 with a fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K7I
- Type
- protein
- Length
- 483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin-5, mitochondrial
- EC
- 1.11.1.15
- UniProt
- P30044
- Ligands
- CAQ
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxiredoxin-5, mitochondrial (EC 1.11.1.15) | protein | 162 | 33% helix, 25% strand | P30044 |
| B | Peroxiredoxin-5, mitochondrial (EC 1.11.1.15) | protein | 161 | 31% helix, 24% strand | P30044 |
| C | Peroxiredoxin-5, mitochondrial (EC 1.11.1.15) | protein | 160 | 26% helix, 24% strand | P30044 |
Ligands and binding sites
- CAQ · Catechol · ligand · 2 copies · chains A, C, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.55 | 0.84 | 23 | empty |
| 2 | 224 | 0.51 | 0.76 | 23 | empty |
| 3 | 131 | 0.46 | 0.77 | 20 | CAQ |
| 4 | 120 | 0.40 | 0.75 | 25 | empty |
| 5 | 51 | 0.25 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- B–C · 792 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
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 P30044
- Elsewhere: RCSB PDB 4K7I · PDBe 4K7I · UniProt P30044
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.