Research workbench
Crystal structure of a ribokinase-like superfamily protein (EF1790) from enterococcus faecalis V583 at 1.80 a resolution
Analyse Crystal structure of a ribokinase-like superfamily protein (EF1790) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R3B
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yjef-related protein
- UniProt
- Q833Y3
- Ligands
- MG, CL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yjef-related protein | protein | 283 | 50% helix, 14% strand | Q833Y3 |
| B | Yjef-related protein | protein | 284 | 50% helix, 14% strand | Q833Y3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
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 | 649 | 0.78 | 0.84 | 64 | CL, EDO |
| 2 | 162 | 0.54 | 0.80 | 23 | EDO |
| 3 | 94 | 0.39 | 0.76 | 18 | empty |
| 4 | 71 | 0.34 | 0.75 | 16 | empty |
| 5 | 62 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1284 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2R3B · CRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF1790) FROM ENTEROCOCCUS… · the same entry in another collection · chain A against A, TM-score 1.00
- Q833Y3 · AlphaFold monomer V2.0 prediction for ADP-dependent (S)-NAD(P)H-hydrate dehydratase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q833Y3
- Elsewhere: RCSB PDB 2R3B · PDBe 2R3B · UniProt Q833Y3
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