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Crystal structure of D-allulose 3-epimerase with D-allulose from agrobacterium sp. SUL3
Analyse Crystal structure of D-allulose 3-epimerase with D-allulose from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ERO
- Type
- protein
- Length
- 1,132 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-tagatose 3-epimerase
- EC
- 5.1.3.-
- UniProt
- A0A0L6K0Q2
- Ligands
- PSJ, MG
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 283 | 47% helix, 15% strand | A0A0L6K0Q2 |
| B | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 284 | 48% helix, 15% strand | A0A0L6K0Q2 |
| C | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 282 | 46% helix, 15% strand | A0A0L6K0Q2 |
Ligands and binding sites
- PSJ · D-psicose · ligand · 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
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.86 | 0.91 | 63 | empty |
| 2 | 352 | 0.70 | 0.83 | 52 | PSJ |
| 3 | 362 | 0.69 | 0.82 | 51 | PSJ |
| 4 | 254 | 0.68 | 0.84 | 36 | PSJ |
| 5 | 249 | 0.66 | 0.83 | 35 | PSJ |
Interfaces
6 interfaces between chains.
- C–D · 1686 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1684 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 594 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 396 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7ERO · Crystal structure of D-allulose 3-epimerase with D-allulose 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 7ERO · PDBe 7ERO · UniProt A0A0L6K0Q2
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