MolNFT v1 · #66693 · protein
Crystal structure of sulfiredoxin in complex with peroxiredoxin I and ATP:MG2+
3HY2 · Peroxiredoxin-1: “Crystal structure of sulfiredoxin in complex with peroxiredoxin I and ATP:MG2+”. X-ray diffraction, 2 ligands (ATP, MG), 5 pockets (best druggability 0.69). MolNFT v1 #66693 on GenesisL1: 3D structure, binding…
- PDB
- 3HY2
- Type
- protein
- Length
- 571 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin-1; Sulfiredoxin-1
- EC
- 1.11.1.15, 1.8.98.2
- UniProt
- Q06830, Q9BYN0
- Ligands
- ATP, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxiredoxin-1 (EC 1.11.1.15) | protein | 185 | 29% helix, 25% strand | Q06830 |
| B | Peroxiredoxin-1 (EC 1.11.1.15) | protein | 184 | 28% helix, 25% strand | Q06830 |
| X, Y | Sulfiredoxin-1 (EC 1.8.98.2) | protein | 101 | 39% helix, 27% strand | Q9BYN0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, X, B, Y
- MG · Magnesium ion · metal · 2 copies · chains A, X, B, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.69 | 0.79 | 53 | MG, ATP |
| 2 | 515 | 0.68 | 0.79 | 56 | MG, ATP |
| 3 | 267 | 0.64 | 0.81 | 51 | empty |
| 4 | 59 | 0.30 | 0.75 | 19 | empty |
| 5 | 54 | 0.28 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–X · 924 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 924 Ų buried · 17 hydrogen bonds · protein-protein
- A–Y · 918 Ų buried · 9 hydrogen bonds · protein-protein
- A–X · 567 Ų buried · 5 hydrogen bonds · protein-protein
- B–Y · 544 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3HY2 · Crystal Structure of Sulfiredoxin in Complex with Peroxiredoxin I and ATP:Mg2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYN0 · AlphaFold monomer V2.0 prediction for sulfiredoxin-1 (Q9BYN0) · a predicted model of the same protein · chain X against A, TM-score 0.96
- Q06830 · AlphaFold monomer V2.0 prediction for peroxiredoxin-1 (Q06830) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 Q06830
- Every structure of UniProt Q9BYN0
- Elsewhere: RCSB PDB 3HY2 · PDBe 3HY2 · UniProt Q06830 · UniProt Q9BYN0
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