Research workbench
Periplasmic edta-binding protein eppa, orthorhombic
Analyse Periplasmic edta-binding protein eppa, orthorhombic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WM7
- Type
- protein
- Length
- 1,070 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein, family 5
- UniProt
- Q11H97
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular solute-binding protein, family 5 | protein | 534 | 30% helix, 23% strand | Q11H97 |
| B | Extracellular solute-binding protein, family 5 | protein | 536 | 30% helix, 23% strand | Q11H97 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.87 | 0.90 | 96 | EDO |
| 2 | 871 | 0.84 | 0.86 | 75 | EDO |
| 3 | 193 | 0.81 | 0.95 | 29 | EDO |
| 4 | 264 | 0.79 | 0.91 | 36 | EDO |
| 5 | 819 | 0.78 | 0.81 | 78 | EDO, SO4 |
Interfaces
1 interface between chains.
- A–B · 1534 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6WM7 · Periplasmic EDTA-binding protein EppA, orthorhombic · 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 Q11H97
- Elsewhere: RCSB PDB 6WM7 · PDBe 6WM7 · UniProt Q11H97
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