MolNFT v1 · #81291 · protein
Crystal structure of a hypothetical peroxiredoxin protein frm sinorhizobium meliloti
3UMA: “Crystal structure of a hypothetical peroxiredoxin protein frm sinorhizobium meliloti”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.64). MolNFT v1 #81291 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3UMA
- Type
- protein
- Length
- 495 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical peroxiredoxin protein
- UniProt
- Q92RF9
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical peroxiredoxin protein | protein | 166 | 30% helix, 31% strand | Q92RF9 |
| B | Hypothetical peroxiredoxin protein | protein | 161 | 30% helix, 32% strand | Q92RF9 |
| C | Hypothetical peroxiredoxin protein | protein | 168 | 30% helix, 30% strand | Q92RF9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
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 | 340 | 0.64 | 0.79 | 59 | empty |
| 2 | 217 | 0.61 | 0.81 | 26 | empty |
| 3 | 77 | 0.36 | 0.76 | 16 | empty |
| 4 | 50 | 0.28 | 0.75 | 14 | empty |
| 5 | 60 | 0.26 | 0.72 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 826 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 579 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3UMA · Crystal structure of a hypothetical peroxiredoxin protein frm Sinorhizobium meliloti · the same entry in another collection · chain B against B, 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 Q92RF9
- Elsewhere: RCSB PDB 3UMA · PDBe 3UMA · UniProt Q92RF9
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