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Crystal structure of D-allulose 3-epimerase with D-fructose from Agrobacterium sp. SUL3
Analyse Crystal structure of D-allulose 3-epimerase with D-fructose from Agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ERN
- Type
- protein
- Length
- 1,133 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Agrobacterium sp. SUL3
- Molecule
- D-tagatose 3-epimerase
- EC
- 5.1.3.-
- UniProt
- A0A0L6K0Q2
- Ligands
- FUD, MG
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.05 · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 283 | 46% helix, 15% strand | A0A0L6K0Q2 |
| C | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 284 | 48% helix, 15% strand | A0A0L6K0Q2 |
Ligands and binding sites
- FUD · D-fructose · sugar · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.86 | 0.90 | 74 | empty |
| 2 | 713 | 0.78 | 0.83 | 81 | FUD |
| 3 | 253 | 0.69 | 0.85 | 34 | FUD |
| 4 | 363 | 0.68 | 0.81 | 51 | FUD |
| 5 | 268 | 0.55 | 0.77 | 40 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1701 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1686 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 626 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 607 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 388 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7ERN · Crystal structure of D-allulose 3-epimerase with D-fructose from agrobacterium sp. SUL3 · 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 A0A0L6K0Q2
- Elsewhere: RCSB PDB 7ERN · PDBe 7ERN · UniProt A0A0L6K0Q2
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