Research workbench
Crystal structure of xyloglucan xylosyltransferase 1 ternary form
Analyse Crystal structure of xyloglucan xylosyltransferase 1 ternary form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BSW
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xyloglucan 6-xylosyltransferase 1
- EC
- 2.4.2.39
- UniProt
- Q9LZJ3
- Ligands
- UDP, BGC, MN, NO3
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xyloglucan 6-xylosyltransferase 1 (EC 2.4.2.39) | protein | 337 | 40% helix, 17% strand | Q9LZJ3 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.74 | 0.82 | 40 | empty |
| 2 | 694 | 0.73 | 0.79 | 60 | BGC, MN, UDP, GOL |
| 3 | 729 | 0.72 | 0.78 | 63 | UDP, NO3 |
| 4 | 182 | 0.66 | 0.85 | 35 | empty |
| 5 | 197 | 0.63 | 0.84 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2993 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6BSW · Crystal structure of Xyloglucan Xylosyltransferase 1 ternary form · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LZJ3 · AlphaFold monomer V2.0 prediction for xyloglucan 6-xylosyltransferase 1 (Q9LZJ3) · a predicted model of the same protein · 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 Q9LZJ3
- Elsewhere: RCSB PDB 6BSW · PDBe 6BSW · UniProt Q9LZJ3
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