Research workbench
Crystal structure of D-tagatose 3-epimerase from pseudomonas cichorii
Analyse Crystal structure of D-tagatose 3-epimerase from pseudomonas cichorii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OU4
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-tagatose 3-epimerase
- EC
- 5.3.1.-
- UniProt
- O50580
- Ligands
- MN
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 290 | 45% helix, 16% strand | O50580 |
| B, C, D | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 289 | 45% helix, 14% strand | O50580 |
Ligands and binding sites
- MN · Manganese (II) 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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.66 | 0.76 | 42 | empty |
| 2 | 328 | 0.66 | 0.81 | 51 | empty |
| 3 | 140 | 0.65 | 0.87 | 31 | empty |
| 4 | 154 | 0.63 | 0.85 | 33 | empty |
| 5 | 185 | 0.62 | 0.83 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1532 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1506 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2OU4 · Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii · the same entry in another collection · chain D against D, TM-score 1.00
- O50580 · AlphaFold monomer V2.0 prediction for D-tagatose 3-epimerase (O50580) · a predicted model of the same protein · 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 O50580
- Elsewhere: RCSB PDB 2OU4 · PDBe 2OU4 · UniProt O50580
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