Research workbench
Enterococcus faecalis fic protein in complex with ADP and calcium ion.
Analyse Enterococcus faecalis fic protein in complex with ADP and calcium ion. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EP2
- Type
- protein
- Length
- 2,430 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fic family protein
- UniProt
- U6S0Y1
- Ligands
- ADP, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, H, I, J | Fic family protein | protein | 202 | 62% helix, 5% strand | U6S0Y1 |
| D, E, G, L | Fic family protein | protein | 203 | 63% helix, 5% strand | U6S0Y1 |
| K | Fic family protein | protein | 204 | 61% helix, 5% strand | U6S0Y1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CA · Calcium ion · metal · 24 copies · chains A, D, B, C, E, L, F, J, G, I, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.88 | 0.90 | 138 | ADP, CA |
| 2 | 1012 | 0.86 | 0.87 | 117 | ADP, CA |
| 3 | 512 | 0.83 | 0.90 | 73 | ADP, CA |
| 4 | 528 | 0.83 | 0.89 | 85 | ADP, CA |
| 5 | 522 | 0.83 | 0.89 | 76 | ADP, CA |
Interfaces
31 interfaces between chains.
- E–L · 1118 Ų buried · 32 hydrogen bonds · protein-protein
- H–K · 1109 Ų buried · 27 hydrogen bonds · protein-protein
- G–I · 1107 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1101 Ų buried · 30 hydrogen bonds · protein-protein
- F–J · 1099 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6EP2 · Enterococcus faecalis FIC protein in complex with ADP and calcium ion. · 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 U6S0Y1
- Elsewhere: RCSB PDB 6EP2 · PDBe 6EP2 · UniProt U6S0Y1
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