MolNFT v1 · #123064 · protein
Crystal structure of D-tagatose 3-epimerase C66S from pseudomonas cichorii in complex with 1-deoxy L-tagatose, using a crystal grown in microgravity
5J8L: “Crystal structure of D-tagatose 3-epimerase C66S from pseudomonas cichorii in complex with 1-deoxy…”. X-ray diffraction, 3 ligands (TGK, TGJ, MN), 11 pockets (best druggability 0.78). MolNFT v1 #123064 on GenesisL1: 3D structure…
- PDB
- 5J8L
- Type
- protein
- Length
- 1,173 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-tagatose 3-epimerase
- EC
- 5.1.3.31
- UniProt
- O50580
- Ligands
- TGK, TGJ, MN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tagatose 3-epimerase (EC 5.1.3.31) | protein | 294 | 45% helix, 16% strand | O50580 |
| B | D-tagatose 3-epimerase (EC 5.1.3.31) | protein | 292 | 45% helix, 16% strand | O50580 |
| C | D-tagatose 3-epimerase (EC 5.1.3.31) | protein | 297 | 43% helix, 16% strand | O50580 |
| D | D-tagatose 3-epimerase (EC 5.1.3.31) | protein | 290 | 46% helix, 17% strand | O50580 |
Ligands and binding sites
- TGK · 1-deoxy-beta-L-tagatopyranose · ligand · 8 copies · chains A, B, C, D
- TGJ · 1-deoxy-L-tagatose · ligand · 2 copies · chains A
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.78 | 0.80 | 126 | TGJ, TGK |
| 2 | 886 | 0.78 | 0.81 | 101 | TGK |
| 3 | 222 | 0.55 | 0.78 | 21 | empty |
| 4 | 116 | 0.44 | 0.77 | 24 | empty |
| 5 | 113 | 0.43 | 0.77 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1552 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1504 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 674 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J8L · Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex… · 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 D 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 5J8L · PDBe 5J8L · UniProt O50580
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