Research workbench
Structure of a glycosyltransferase / state 2
Analyse Structure of a glycosyltransferase / state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EJJ
- Type
- protein
- Length
- 720 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wlac protein
- UniProt
- O86151
- Ligands
- UDP, BUE, A2G, NDG, NA, CL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Wlac protein | protein | 360 | 45% helix, 18% strand | O86151 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- BUE · NerylNeryl pyrophosphate · ligand · 2 copies · chains A, B
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.75 | 0.82 | 66 | A2G, UDP, NA, CL |
| 2 | 511 | 0.74 | 0.82 | 63 | A2G, UDP, NA |
| 3 | 213 | 0.57 | 0.79 | 35 | empty |
| 4 | 287 | 0.52 | 0.75 | 44 | empty |
| 5 | 106 | 0.40 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 709 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6EJJ · Structure of a glycosyltransferase / state 2 · 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 O86151
- Elsewhere: RCSB PDB 6EJJ · PDBe 6EJJ · UniProt O86151
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