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The crystal structure of the protein of degv family COG1307 with unknown function from ruminococcus gnavus atcc 29149
Analyse The crystal structure of the protein of degv family COG1307 with unknown… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JR7
- Type
- protein
- Length
- 558 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized egv family protein COG1307
- UniProt
- A7B6P0
- Ligands
- NA, PO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized egv family protein COG1307 | protein | 279 | 41% helix, 24% strand | A7B6P0 |
| B | Uncharacterized egv family protein COG1307 | protein | 279 | 39% helix, 24% strand | A7B6P0 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.80 | 0.96 | 29 | PG6 |
| 2 | 151 | 0.79 | 0.95 | 29 | PG6 |
| 3 | 356 | 0.59 | 0.76 | 32 | empty |
| 4 | 156 | 0.50 | 0.78 | 24 | empty |
| 5 | 150 | 0.47 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 3JR7 · The crystal structure of the protein of DegV family COG1307 with unknown function 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 A7B6P0
- Elsewhere: RCSB PDB 3JR7 · PDBe 3JR7 · UniProt A7B6P0
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