Research workbench
Crystal structure of the mitochondrial peroxiredoxin from leishmania braziliensis in the decameric form
Analyse Crystal structure of the mitochondrial peroxiredoxin from leishmania… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KB3
- Type
- protein
- Length
- 1,647 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxidoxin
- EC
- 1.11.1.-
- UniProt
- A4HCL7
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, G, I, J | Peroxidoxin (EC 1.11.1.-) | protein | 163 | 31% helix, 29% strand | A4HCL7 |
| B, D | Peroxidoxin (EC 1.11.1.-) | protein | 169 | 29% helix, 28% strand | A4HCL7 |
| C | Peroxidoxin (EC 1.11.1.-) | protein | 162 | 30% helix, 28% strand | A4HCL7 |
| H | Peroxidoxin (EC 1.11.1.-) | protein | 169 | 29% helix, 28% strand | A4HCL7 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.76 | 0.98 | 24 | empty |
| 2 | 73 | 0.75 | 0.99 | 23 | empty |
| 3 | 73 | 0.75 | 0.98 | 22 | empty |
| 4 | 71 | 0.75 | 0.98 | 23 | empty |
| 5 | 71 | 0.74 | 0.98 | 23 | empty |
Interfaces
10 interfaces between chains.
- G–H · 1262 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1172 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1165 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 999 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 977 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4KB3 · Crystal structure of the mitochondrial peroxiredoxin from Leishmania braziliensis in the… · 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 A4HCL7
- Elsewhere: RCSB PDB 4KB3 · PDBe 4KB3 · UniProt A4HCL7
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