Research workbench
Crystal structure of human udp-xylose synthase.
Analyse Crystal structure of human udp-xylose synthase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GLL
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucuronic acid decarboxylase 1
- EC
- 4.1.1.35
- UniProt
- Q8NBZ7
- Ligands
- NAD, GAI, SO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 307 | 41% helix, 19% strand | Q8NBZ7 |
| B | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 306 | 40% helix, 18% strand | Q8NBZ7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- GAI · Guanidine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.82 | 0.88 | 68 | NAD, GAI, SO4 |
| 2 | 704 | 0.79 | 0.83 | 76 | NAD |
| 3 | 107 | 0.38 | 0.75 | 22 | empty |
| 4 | 106 | 0.37 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1519 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
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 Q8NBZ7
- Elsewhere: RCSB PDB 4GLL · PDBe 4GLL · UniProt Q8NBZ7
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