MolNFT v1 · #111539 · protein
Crystal structure of D-tagatose 3-epimerase C66S from pseudomonas cichorii in complex with 6-deoxy L-psicose
4YTT: “Crystal structure of D-tagatose 3-epimerase C66S from pseudomonas cichorii in complex with 6-deoxy L-psicose”. X-ray diffraction, 3 ligands (PUD, PUF, MN), 10 pockets (best druggability 0.75). MolNFT v1 #111539 on GenesisL1: 3D…
- PDB
- 4YTT
- 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
- PUD, PUF, MN
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 294 | 44% helix, 16% strand | O50580 |
| B | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 290 | 44% helix, 17% strand | O50580 |
| C | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 297 | 44% helix, 16% strand | O50580 |
| D | D-tagatose 3-epimerase (EC 5.3.1.-) | protein | 292 | 45% helix, 15% strand | O50580 |
Ligands and binding sites
- PUD · 6-deoxy-L-psicose · ligand · 4 copies · chains A, B, C, D
- PUF · 6-deoxy-alpha-L-psicofuranose · ligand · 3 copies · chains A, B, 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.75 | 0.79 | 91 | PUD |
| 2 | 661 | 0.72 | 0.79 | 72 | PUD |
| 3 | 154 | 0.65 | 0.87 | 32 | PUD |
| 4 | 166 | 0.64 | 0.85 | 31 | PUD |
| 5 | 189 | 0.56 | 0.80 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1503 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1478 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 672 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YTT · 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 B 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 4YTT · PDBe 4YTT · UniProt O50580
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