MolNFT v1 · #74820 · protein
Crystal structure of an atypical two-cysteine peroxiredoxin (SAOUHSC_01822) from staphylococcus aureus NCTC8325
3P7X · Probable thiol peroxidase: “Crystal structure of an atypical two-cysteine peroxiredoxin (SAOUHSC_01822) from staphylococcus aureus…”. X-ray diffraction, 2 ligands (DTV, SO4), 5 pockets (best druggability 0.51). MolNFT v1 #74820 on…
- PDB
- 3P7X
- Type
- protein
- Length
- 655 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable thiol peroxidase
- EC
- 1.11.1.-
- UniProt
- Q2FXL3
- Ligands
- DTV, SO4
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable thiol peroxidase (EC 1.11.1.-) | protein | 166 | 26% helix, 28% strand | Q2FXL3 |
| B, C, D | Probable thiol peroxidase (EC 1.11.1.-) | protein | 163 | 26% helix, 30% strand | Q2FXL3 |
Ligands and binding sites
- DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 15 copies · chains A, B, D, C
- DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.51 | 0.74 | 37 | PG4 |
| 2 | 80 | 0.35 | 0.75 | 19 | PG4 |
| 3 | 55 | 0.32 | 0.76 | 22 | empty |
| 4 | 58 | 0.31 | 0.75 | 18 | empty |
| 5 | 52 | 0.30 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 763 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 759 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 386 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3P7X · Crystal structure of an atypical two-cysteine peroxiredoxin (SAOUHSC_01822) from… · 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 Q2FXL3
- Elsewhere: RCSB PDB 3P7X · PDBe 3P7X · UniProt Q2FXL3
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