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Crystal structure of D-tagatose 3-epimerase from pseudomonas cichorii with D-tagatose
Analyse Crystal structure of D-tagatose 3-epimerase from pseudomonas cichorii with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QUM
- Type
- protein
- Length
- 1,160 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
- TAG, MN
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 290 | 45% helix, 16% strand | O50580 |
Ligands and binding sites
- TAG · D-tagatose · ligand · 4 copies · chains A, B, C, D
- 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.74 | 0.78 | 99 | TAG |
| 2 | 722 | 0.74 | 0.80 | 82 | TAG |
| 3 | 149 | 0.65 | 0.86 | 31 | TAG |
| 4 | 142 | 0.63 | 0.86 | 28 | TAG |
| 5 | 174 | 0.53 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1540 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1494 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 707 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2QUM · Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii with D-tagatose · the same entry in another collection · chain C against C, 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 2QUM · PDBe 2QUM · UniProt O50580
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