Research workbench
The crystal structure E. COLI spy
Analyse The crystal structure E. COLI spy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OEO
- Type
- protein
- Length
- 364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spheroplast protein Y
- UniProt
- C5W4R8
- Ligands
- CD
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Spheroplast protein Y | protein | 91 | 66% helix, 0% strand | C5W4R8 |
Ligands and binding sites
- CD · Cadmium ion · metal · 22 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.59 | 0.77 | 43 | empty |
| 2 | 348 | 0.59 | 0.76 | 50 | CD |
| 3 | 97 | 0.45 | 0.79 | 15 | empty |
| 4 | 97 | 0.43 | 0.78 | 13 | empty |
| 5 | 79 | 0.40 | 0.78 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1573 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1487 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 297 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 233 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 181 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3OEO · The crystal structure E. coli Spy · 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 C5W4R8
- Elsewhere: RCSB PDB 3OEO · PDBe 3OEO · UniProt C5W4R8
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