MolNFT v1 · #49651 · protein
Crystal structure of D-tagatose 3-epimerase from pseudomonas cichorii in complex with D-fructose
2QUN: “Crystal structure of D-tagatose 3-epimerase from pseudomonas cichorii in complex with D-fructose”. X-ray diffraction, 2 ligands (FUD, MN), 9 pockets (best druggability 0.77). MolNFT v1 #49651 on GenesisL1: 3D structure, binding…
- PDB
- 2QUN
- 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
- FUD, MN
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 44% 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 | 44% helix, 16% strand | O50580 |
Ligands and binding sites
- FUD · D-fructose · 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.77 | 0.79 | 113 | FUD |
| 2 | 838 | 0.75 | 0.79 | 100 | FUD |
| 3 | 152 | 0.64 | 0.86 | 32 | FUD |
| 4 | 156 | 0.63 | 0.85 | 31 | FUD |
| 5 | 178 | 0.54 | 0.79 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1507 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1491 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 682 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2QUN · Crystal Structure of D-tagatose 3-epimerase from Pseudomonas cichorii in Complex with… · 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 2QUN · PDBe 2QUN · UniProt O50580
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