Research workbench
Crystal structure of the putative ALPHA/BETA hydrolase rutd from E.COLI
Analyse Crystal structure of the putative ALPHA/BETA hydrolase rutd from E.COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V48
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aminoacrylate hydrolase rutd
- EC
- 3.5.1.-
- UniProt
- B6I985
- Ligands
- SCN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aminoacrylate hydrolase rutd (EC 3.5.1.-) | protein | 268 | 51% helix, 15% strand | B6I985 |
| B | Putative aminoacrylate hydrolase rutd (EC 3.5.1.-) | protein | 263 | 50% helix, 14% strand | B6I985 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.76 | 0.86 | 41 | GOL, SCN |
| 2 | 351 | 0.75 | 0.86 | 43 | GOL |
| 3 | 67 | 0.33 | 0.76 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 1405 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3V48 · Crystal Structure of the putative alpha/beta hydrolase RutD from E.coli · the same entry in another collection · chain A against A, TM-score 1.00
- B6I985 · AlphaFold monomer V2.0 prediction for putative aminoacrylate hydrolase rutd (B6I985) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 B6I985
- Elsewhere: RCSB PDB 3V48 · PDBe 3V48 · UniProt B6I985
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