MolNFT v1 · #111538 · protein
Crystal structure of D-tagatose 3-epimerase C66S from pseudomonas cichorii in complex with 1-deoxy 3-keto D-galactitol
4YTS: “Crystal structure of D-tagatose 3-epimerase C66S from pseudomonas cichorii in complex with 1-deoxy 3-keto…”. X-ray diffraction, 3 ligands (TGS, TGR, MN), 11 pockets (best druggability 0.74). MolNFT v1 #111538 on GenesisL1: 3D…
- PDB
- 4YTS
- 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
- 5.3.1.-
- UniProt
- O50580
- Ligands
- TGS, TGR, MN
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 294 | 45% helix, 16% strand | O50580 |
| B | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 292 | 44% helix, 16% strand | O50580 |
| C | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 297 | 44% helix, 14% strand | O50580 |
| D | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 290 | 45% helix, 15% strand | O50580 |
Ligands and binding sites
- TGS · 1-deoxy-D-xylo-hex-3-ulose · ligand · 9 copies · chains A, B, C, D
- TGR · 1-deoxy-alpha-D-xylo-hex-3-ulofuranose · ligand · 3 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 | 773 | 0.74 | 0.79 | 85 | TGS |
| 2 | 719 | 0.72 | 0.79 | 85 | TGS, TGR |
| 3 | 160 | 0.68 | 0.88 | 30 | TGS |
| 4 | 194 | 0.65 | 0.84 | 32 | TGS |
| 5 | 202 | 0.53 | 0.78 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1508 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1502 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 661 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YTS · Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex… · 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 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 4YTS · PDBe 4YTS · UniProt O50580
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