Research workbench
Crystal structures of D-allulose 3-epimerase with D-sorbose from sinorhizobium fredii
Analyse Crystal structures of D-allulose 3-epimerase with D-sorbose from sinorhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DZ5
- Type
- protein
- Length
- 1,130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-tagatose 3-epimerase
- UniProt
- A0A249Q1V1
- Ligands
- SDD, HVC, MG
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-tagatose 3-epimerase | protein | 283 | 45% helix, 15% strand | A0A249Q1V1 |
| B, D | D-tagatose 3-epimerase | protein | 282 | 45% helix, 15% strand | A0A249Q1V1 |
Ligands and binding sites
- SDD · D-sorbose · ligand · 4 copies · chains A, B, C, D
- HVC · alpha-D-Sorbopyranose · ligand · 3 copies · chains A, 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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.87 | 0.93 | 57 | empty |
| 2 | 74 | 0.75 | 0.98 | 23 | SDD |
| 3 | 71 | 0.74 | 0.98 | 23 | SDD |
| 4 | 311 | 0.69 | 0.83 | 45 | SDD |
| 5 | 260 | 0.69 | 0.84 | 34 | SDD |
Interfaces
6 interfaces between chains.
- B–C · 1642 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1635 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 571 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 567 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 423 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7DZ5 · Crystal structures of D-allulose 3-epimerase with D-sorbose from Sinorhizobium fredii · 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 A0A249Q1V1
- Elsewhere: RCSB PDB 7DZ5 · PDBe 7DZ5 · UniProt A0A249Q1V1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.