MolNFT v1 · #99885 · protein
Crystal structure of bovine mitochondrial peroxiredoxin III
4MH3 · Thioredoxin-dependent peroxide reductase, mitochondrial: “Crystal structure of bovine mitochondrial peroxiredoxin III”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.78). MolNFT v1 #99885 on GenesisL1: 3D…
- PDB
- 4MH3
- Type
- protein
- Length
- 2,006 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin-dependent peroxide reductase, mitochondrial
- EC
- 1.11.1.15
- UniProt
- P35705
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1.11.1.15) | protein | 166 | 31% helix, 29% strand | P35705 |
| B, D | Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1.11.1.15) | protein | 168 | 28% helix, 29% strand | P35705 |
| C | Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1.11.1.15) | protein | 169 | 30% helix, 28% strand | P35705 |
| E | Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1.11.1.15) | protein | 164 | 29% helix, 29% strand | P35705 |
| F, K | Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1.11.1.15) | protein | 168 | 30% helix, 29% strand | P35705 |
| G | Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1.11.1.15) | protein | 168 | 28% helix, 29% strand | P35705 |
| H, I, L | Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1.11.1.15) | protein | 167 | 31% helix, 29% strand | P35705 |
| J | Thioredoxin-dependent peroxide reductase, mitochondrial (EC 1.11.1.15) | protein | 166 | 31% helix, 30% strand | P35705 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains J, K
- CIT · Citric acid · additive · 3 copies · chains A, B, C, D, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.78 | 0.98 | 21 | empty |
| 2 | 84 | 0.77 | 0.99 | 21 | empty |
| 3 | 95 | 0.76 | 0.98 | 22 | CIT |
| 4 | 87 | 0.76 | 0.98 | 19 | CIT |
| 5 | 83 | 0.75 | 0.98 | 22 | CIT |
Interfaces
12 interfaces between chains.
- C–D · 1320 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 1306 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 1162 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1148 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1067 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4MH3 · Crystal structure of Bovine Mitochondrial Peroxiredoxin III · the same entry in another collection · chain L against L, 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 P35705
- Elsewhere: RCSB PDB 4MH3 · PDBe 4MH3 · UniProt P35705
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