MolNFT v1 · #24183 · protein
Xyloglucan endotransglycosylase in complex with the xyloglucan nonasaccharide xllg.
1UMZ: “Xyloglucan endotransglycosylase in complex with the xyloglucan nonasaccharide xllg.”. X-ray diffraction, 5 ligands (BGC, NAG, XYS), 4 pockets (best druggability 0.67). MolNFT v1 #24183 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1UMZ
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xyloglucan endotransglycosylase
- EC
- 2.4.1.207
- UniProt
- Q8GZD5
- Ligands
- BGC, NAG, XYS, BMA, GAL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xyloglucan endotransglycosylase (EC 2.4.1.207) | protein | 267 | 18% helix, 39% strand | Q8GZD5 |
| B | Xyloglucan endotransglycosylase (EC 2.4.1.207) | protein | 264 | 16% helix, 40% strand | Q8GZD5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.67 | 0.78 | 61 | BGC |
| 2 | 101 | 0.40 | 0.76 | 19 | empty |
| 3 | 68 | 0.35 | 0.76 | 19 | empty |
| 4 | 58 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 416 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1UMZ · Xyloglucan endotransglycosylase in complex with the xyloglucan nonasaccharide XLLG. · 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 Q8GZD5
- Elsewhere: RCSB PDB 1UMZ · PDBe 1UMZ · UniProt Q8GZD5
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