Research workbench
Structure of phytolacca americana UGT2 complexed with udp-2FLUORO- glucose and pterostilbene
Analyse Structure of phytolacca americana UGT2 complexed with udp-2FLUORO- glucose and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JEN
- Type
- protein
- Length
- 1,309 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase
- EC
- 2.4.1.-
- UniProt
- B5MGN7
- Ligands
- 3RL, U2F
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase (EC 2.4.1.-) | protein | 440 | 47% helix, 14% strand | B5MGN7 |
| B | Glycosyltransferase (EC 2.4.1.-) | protein | 433 | 48% helix, 14% strand | B5MGN7 |
| C | Glycosyltransferase (EC 2.4.1.-) | protein | 436 | 46% helix, 14% strand | B5MGN7 |
Ligands and binding sites
- 3RL · Pterostilbene · ligand · 3 copies · chains A, B, C
- U2F · Uridine-5'-diphosphate-2-deoxy-2-fluoro-alpha-D-glucose · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.77 | 0.81 | 64 | 3RL, U2F |
| 2 | 743 | 0.77 | 0.81 | 79 | 3RL, U2F |
| 3 | 732 | 0.76 | 0.81 | 70 | 3RL, U2F |
| 4 | 356 | 0.58 | 0.75 | 53 | empty |
| 5 | 392 | 0.56 | 0.74 | 46 | empty |
Interfaces
2 interfaces between chains.
- A–B · 754 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 210 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6JEN · Structure of Phytolacca americana UGT2 complexed with UDP-2fluoro-glucose and… · the same entry in another collection · 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 B5MGN7
- Elsewhere: RCSB PDB 6JEN · PDBe 6JEN · UniProt B5MGN7
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