Research workbench
Crystal structure of a sugar phosphate ISOMERASE/EPIMERASE (BDI_3400) from parabacteroides distasonis atcc 8503 at 1.70 a resolution
Analyse Crystal structure of a sugar phosphate ISOMERASE/EPIMERASE (BDI_3400) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OBE
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar phosphate ISOMERASE/EPIMERASE
- UniProt
- A6LHD8
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar phosphate ISOMERASE/EPIMERASE | protein | 286 | 41% helix, 16% strand | A6LHD8 |
| B | Sugar phosphate ISOMERASE/EPIMERASE | protein | 290 | 40% helix, 16% strand | A6LHD8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EOH · Ethanol · additive · 10 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.50 | 0.77 | 25 | empty |
| 2 | 119 | 0.44 | 0.77 | 17 | empty |
| 3 | 135 | 0.42 | 0.75 | 26 | PO4, EOH |
| 4 | 58 | 0.39 | 0.80 | 14 | EOH |
| 5 | 77 | 0.37 | 0.77 | 20 | EOH |
Interfaces
1 interface between chains.
- A–B · 806 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3OBE · Crystal structure of a sugar phosphate isomerase/epimerase (BDI_3400) from… · 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 A6LHD8
- Elsewhere: RCSB PDB 3OBE · PDBe 3OBE · UniProt A6LHD8
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