MolNFT v1 · #49649 · protein
Crystal structure of D-tagatose 3-epimerase from pseudomonas cichorii at 1.79 a resolution
2QUL: “Crystal structure of D-tagatose 3-epimerase from pseudomonas cichorii at 1.79 a resolution”. X-ray diffraction, 1 ligand (MN), 9 pockets (best druggability 0.77). MolNFT v1 #49649 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2QUL
- 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
- 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
- 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 | 862 | 0.77 | 0.80 | 89 | empty |
| 2 | 825 | 0.74 | 0.79 | 99 | empty |
| 3 | 144 | 0.63 | 0.86 | 31 | empty |
| 4 | 145 | 0.60 | 0.84 | 30 | empty |
| 5 | 183 | 0.54 | 0.79 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1522 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1487 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2QUL · Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii at 1.79 A resolution · 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 2QUL · PDBe 2QUL · UniProt O50580
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