Research workbench
X-ray structure of cellulomonas parahominis L-ribose isomerase with L- ribose
Analyse X-ray structure of cellulomonas parahominis L-ribose isomerase with L- ribose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WW1
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ribose isomerase
- UniProt
- L0N3Y0
- Ligands
- ROR, 0MK, MN
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-ribose isomerase | protein | 242 | 19% helix, 29% strand | L0N3Y0 |
Ligands and binding sites
- ROR · L-ribose · ligand · chains B
- 0MK · beta-L-ribopyranose · sugar · 3 copies · chains A, 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.68 | 0.97 | 19 | ROR |
| 2 | 324 | 0.58 | 0.77 | 48 | empty |
| 3 | 240 | 0.55 | 0.78 | 40 | empty |
| 4 | 87 | 0.37 | 0.76 | 25 | empty |
| 5 | 61 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2285 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3WW1 · X-ray structure of Cellulomonas parahominis L-ribose isomerase with L-ribose · 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 3WW1 · PDBe 3WW1 · UniProt L0N3Y0
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