Research workbench
Structure of a FIC-domain protein from Mycobacterium marinum in complex with CDP
Analyse Structure of a FIC-domain protein from Mycobacterium marinum in complex with CDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CB8
- Type
- protein
- Length
- 787 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Mycobacterium marinum (strain ATCC BAA-535 / M)
- Molecule
- Fic-domain containing protein
- UniProt
- B2HP08
- Ligands
- CDP, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.6 · 2 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fic-domain containing protein | protein | 394 | 57% helix, 7% strand | B2HP08 |
| B | Fic-domain containing protein | protein | 393 | 56% helix, 7% strand | B2HP08 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- ACT · Acetate ion · additive · 5 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.79 | 0.83 | 63 | ACT, CDP, EDO |
| 2 | 357 | 0.70 | 0.83 | 50 | CDP |
| 3 | 199 | 0.53 | 0.78 | 37 | SO4 |
| 4 | 219 | 0.51 | 0.76 | 34 | ACT, SO4 |
| 5 | 75 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 859 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7CB8 · Structure of a fic-domain protein from mycobacterium marinum in complex with cdp · 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 B2HP08
- Elsewhere: RCSB PDB 7CB8 · PDBe 7CB8 · UniProt B2HP08
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