Research workbench
Crystal structure of the full-length sorbitol operon regulator sorc from klebsiella pneumoniae
Analyse Crystal structure of the full-length sorbitol operon regulator sorc from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W48
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorbitol operon regulator
- UniProt
- P37078
- Ligands
- CL
- Pockets
- 19 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorbitol operon regulator | protein | 308 | 47% helix, 17% strand | P37078 |
| B | Sorbitol operon regulator | protein | 313 | 49% helix, 16% strand | P37078 |
| C | Sorbitol operon regulator | protein | 299 | 46% helix, 16% strand | P37078 |
| D | Sorbitol operon regulator | protein | 308 | 46% helix, 17% strand | P37078 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.70 | 0.88 | 31 | empty |
| 2 | 138 | 0.69 | 0.90 | 30 | GOL |
| 3 | 263 | 0.69 | 0.84 | 37 | GOL |
| 4 | 299 | 0.67 | 0.82 | 36 | empty |
| 5 | 250 | 0.65 | 0.82 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1342 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1143 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 868 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 839 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2W48 · Crystal structure of the Full-length Sorbitol Operon Regulator SorC from Klebsiella… · the same entry in another collection · chain D against D, TM-score 1.00
- P37078 · AlphaFold monomer V2.0 prediction for sorbitol operon regulator (P37078) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P37078
- Elsewhere: RCSB PDB 2W48 · PDBe 2W48 · UniProt P37078
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