MolNFT v1 · #136930 · protein
The crystal structure of the protein of degv family COG1307 from ruminococcus gnavus atcc 29149 (alternative refinement of pdb 3JR7 with vaccenic acid)
5V85 · Edd domain protein, degv family: “The crystal structure of the protein of degv family COG1307 from ruminococcus gnavus atcc 29149 (alternative…”. X-ray diffraction, 3 ligands (VCA, NA, PO4), 10 pockets (best druggability 0.80).…
- PDB
- 5V85
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Edd domain protein, degv family
- UniProt
- A7B6P0
- Ligands
- VCA, NA, PO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Edd domain protein, degv family | protein | 278 | 40% helix, 24% strand | A7B6P0 |
| B | Edd domain protein, degv family | protein | 279 | 39% helix, 24% strand | A7B6P0 |
Ligands and binding sites
- VCA · Vaccenic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.80 | 0.96 | 29 | VCA |
| 2 | 158 | 0.79 | 0.95 | 29 | VCA |
| 3 | 351 | 0.59 | 0.76 | 33 | empty |
| 4 | 161 | 0.52 | 0.79 | 23 | empty |
| 5 | 182 | 0.47 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 602 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 5V85 · The crystal structure of the protein of DegV family COG1307 from Ruminococcus gnavus ATCC… · 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 5V85 · PDBe 5V85 · UniProt A7B6P0
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