Research workbench
Epidermin biosynthesis protein epid from staphylococcus aureus
Analyse Epidermin biosynthesis protein epid from staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QJG
- Type
- protein
- Length
- 2,041 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermin biosynthesis protein epid
- UniProt
- Q5HEV4
- Ligands
- FMN, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermin biosynthesis protein epid | protein | 171 | 44% helix, 25% strand | Q5HEV4 |
| B, C, D, E, F, G, H, I, J, K, L | Epidermin biosynthesis protein epid | protein | 170 | 41% helix, 24% strand | Q5HEV4 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 12 copies · chains A, C, D, B, K, I, E, F, L, H, G, J
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, F, E, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.86 | 0.87 | 107 | CL, FMN |
| 2 | 1002 | 0.85 | 0.86 | 108 | FMN, CL |
| 3 | 1110 | 0.84 | 0.85 | 105 | FMN |
| 4 | 408 | 0.80 | 0.89 | 53 | FMN |
| 5 | 340 | 0.80 | 0.90 | 46 | FMN, CL |
Interfaces
30 interfaces between chains.
- J–L · 888 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 873 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 870 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 866 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 864 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3QJG · Epidermin biosynthesis protein EpiD from Staphylococcus aureus · 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 Q5HEV4
- Elsewhere: RCSB PDB 3QJG · PDBe 3QJG · UniProt Q5HEV4
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