Research workbench
Crystal structure of human udp-xylose synthase R236A substitution
Analyse Crystal structure of human udp-xylose synthase R236A substitution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LK3
- Type
- protein
- Length
- 1,615 residues
- Chains
- 6
- 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, UGA, UDP, POP, SO4
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 267 | 43% helix, 19% strand | Q8NBZ7 |
| B | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 274 | 43% helix, 19% strand | Q8NBZ7 |
| C | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 271 | 43% helix, 19% strand | Q8NBZ7 |
| D | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 273 | 42% helix, 19% strand | Q8NBZ7 |
| E | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 269 | 42% helix, 19% strand | Q8NBZ7 |
| F | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 261 | 44% helix, 17% strand | Q8NBZ7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- UGA · Uridine-5'-diphosphate-glucuronic acid · ligand · 6 copies · chains A, B, C, D, E, F
- UDP · Uridine-5'-diphosphate · ligand · 3 copies · chains A, B, D
- POP · Pyrophosphate 2- · ligand · 3 copies · chains C, E, F
- SO4 · Sulfate ion · ion · 9 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.79 | 0.82 | 69 | NAD, SO4 |
| 2 | 783 | 0.78 | 0.82 | 69 | SO4, NAD |
| 3 | 1136 | 0.78 | 0.80 | 94 | NAD, SO4 |
| 4 | 780 | 0.78 | 0.82 | 71 | NAD, SO4 |
| 5 | 422 | 0.73 | 0.83 | 40 | NAD |
Interfaces
6 interfaces between chains.
- E–F · 812 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 804 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 796 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 754 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 725 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4LK3 · Crystal structure of Human UDP-xylose synthase R236A substitution · the same entry in another collection · chain F against F, TM-score 1.00
- Q8NBZ7 · AlphaFold monomer V2.0 prediction for udp-glucuronic acid decarboxylase 1 (Q8NBZ7) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 4LK3 · PDBe 4LK3 · UniProt Q8NBZ7
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