MolNFT v1 · #62431 · protein
Crystal structure of probable sor operon regulator from shigella flexneri
3EFB · Probable sor-operon regulator: “Crystal structure of probable sor operon regulator from shigella flexneri”. X-ray diffraction, 12 pockets (best druggability 0.66). MolNFT v1 #62431 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3EFB
- Type
- protein
- Length
- 962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable sor-operon regulator
- UniProt
- Q83PA8
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable sor-operon regulator | protein | 246 | 42% helix, 17% strand | Q83PA8 |
| B | Probable sor-operon regulator | protein | 235 | 44% helix, 18% strand | Q83PA8 |
| C | Probable sor-operon regulator | protein | 233 | 42% helix, 19% strand | Q83PA8 |
| D | Probable sor-operon regulator | protein | 248 | 44% helix, 18% strand | Q83PA8 |
Ligands and binding sites
- ACY · Acetic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.66 | 0.75 | 68 | empty |
| 2 | 287 | 0.65 | 0.82 | 45 | empty |
| 3 | 194 | 0.64 | 0.84 | 28 | ACY |
| 4 | 370 | 0.62 | 0.78 | 43 | empty |
| 5 | 132 | 0.55 | 0.82 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–D · 865 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 861 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 495 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3EFB · Crystal Structure of Probable sor Operon Regulator from Shigella flexneri · 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 Q83PA8
- Elsewhere: RCSB PDB 3EFB · PDBe 3EFB · UniProt Q83PA8
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