Research workbench
Epidermicin antimicrobial protein from staphylococcus epidermidis
Analyse Epidermicin antimicrobial protein from staphylococcus epidermidis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SIF
- Type
- protein
- Length
- 401 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermicin locus structural protein
- UniProt
- H9BG66
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 82% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Epidermicin locus structural protein | protein | 51 | 82% helix, 2% strand | H9BG66 |
| D | Epidermicin locus structural protein | protein | 50 | 82% helix, 0% strand | H9BG66 |
| E, H | Epidermicin locus structural protein | protein | 50 | 82% helix, 2% strand | H9BG66 |
| G | Epidermicin locus structural protein | protein | 47 | 81% helix, 0% strand | H9BG66 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains B, G, D, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.69 | 0.79 | 54 | empty |
| 2 | 402 | 0.67 | 0.79 | 41 | empty |
| 3 | 199 | 0.44 | 0.73 | 24 | empty |
| 4 | 84 | 0.36 | 0.75 | 10 | empty |
| 5 | 58 | 0.33 | 0.76 | 13 | empty |
Interfaces
14 interfaces between chains.
- B–C · 388 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 377 Ų buried · 0 hydrogen bonds · protein-protein
- A–G · 332 Ų buried · 1 hydrogen bond · protein-protein
- E–H · 256 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 188 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6SIF · Epidermicin antimicrobial protein from Staphylococcus epidermidis · the same entry in another collection · chain E against E, 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 H9BG66
- Elsewhere: RCSB PDB 6SIF · PDBe 6SIF · UniProt H9BG66
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