MolNFT v1 · #37639 · protein
Conserved degv-like protein of unknown function from streptococcus pyogenes M1 gas binds long-chain fatty acids
2G7Z · Conserved hypothetical protein SPY1493: “Conserved degv-like protein of unknown function from streptococcus pyogenes M1 gas binds long-chain fatty…”. X-ray diffraction, 3 ligands (HXA, ZN, CL), 6 pockets (best druggability 0.80).…
- PDB
- 2G7Z
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical protein SPY1493
- UniProt
- P67372
- Ligands
- HXA, ZN, CL
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved hypothetical protein SPY1493 | protein | 275 | 41% helix, 28% strand | P67372 |
| B | Conserved hypothetical protein SPY1493 | protein | 275 | 41% helix, 28% strand | P67372 |
Ligands and binding sites
- HXA · Docosa-4,7,10,13,16,19-hexaenoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 16 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.80 | 0.96 | 29 | HXA |
| 2 | 143 | 0.78 | 0.95 | 29 | HXA |
| 3 | 163 | 0.57 | 0.82 | 25 | empty |
| 4 | 158 | 0.50 | 0.78 | 26 | empty |
| 5 | 129 | 0.47 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 609 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2G7Z · Conserved DegV-like Protein of Unknown Function from Streptococcus pyogenes M1 GAS Binds… · the same entry in another collection · chain A against A, TM-score 1.00
- P67372 · AlphaFold monomer V2.0 prediction for degv domain-containing protein… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P67372
- Elsewhere: RCSB PDB 2G7Z · PDBe 2G7Z · UniProt P67372
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