Research workbench
X-ray structures of cellulomonas parahominis L-ribose isomerase with L-psicose
Analyse X-ray structures of cellulomonas parahominis L-ribose isomerase with L-psicose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WW2
- Type
- protein
- Length
- 481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ribose isomerase
- UniProt
- L0N3Y0
- Ligands
- SF6, LPK, SF9, MN
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-ribose isomerase | protein | 241 | 19% helix, 28% strand | L0N3Y0 |
| B | L-ribose isomerase | protein | 240 | 20% helix, 29% strand | L0N3Y0 |
Ligands and binding sites
- SF6 · alpha-L-psicofuranose · ligand · chains A
- LPK · L-psicose · ligand · chains B
- SF9 · beta-L-psicofuranose · ligand · chains B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.69 | 0.96 | 20 | LPK |
| 2 | 54 | 0.68 | 0.97 | 21 | SF6 |
| 3 | 198 | 0.50 | 0.77 | 37 | empty |
| 4 | 136 | 0.44 | 0.76 | 30 | empty |
| 5 | 75 | 0.34 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2307 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3WW2 · X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-psicose · 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 L0N3Y0
- Elsewhere: RCSB PDB 3WW2 · PDBe 3WW2 · UniProt L0N3Y0
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