Research workbench
The crystal structure of the protein of degv family COG1307 from ruminococcus gnavus atcc 29149 (alternative refinement of pdb 3JR7 with vaccenic acid)
Analyse The crystal structure of the protein of degv family COG1307 from ruminococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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