Research workbench
Crystal structure of human udp-xylose synthase R236H substitution
Analyse Crystal structure of human udp-xylose synthase R236H substitution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M55
- Type
- protein
- Length
- 1,412 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, POP, UDP, SO4
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 263 | 44% helix, 19% strand | Q8NBZ7 |
| B | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 272 | 43% helix, 18% 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 | 261 | 44% helix, 19% strand | Q8NBZ7 |
| E | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 164 | 42% helix, 20% strand | Q8NBZ7 |
| F | Udp-glucuronic acid decarboxylase 1 (EC 4.1.1.35) | protein | 181 | 56% helix, 0% strand | Q8NBZ7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B, C, D
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.78 | 0.86 | 42 | NAD |
| 2 | 446 | 0.77 | 0.86 | 42 | NAD |
| 3 | 919 | 0.75 | 0.78 | 98 | SO4 |
| 4 | 477 | 0.73 | 0.82 | 43 | NAD |
| 5 | 588 | 0.73 | 0.81 | 44 | NAD |
Interfaces
6 interfaces between chains.
- C–D · 807 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 805 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 803 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 797 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 723 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4M55 · Crystal structure of Human UDP-xylose synthase R236H 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 0.99
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 4M55 · PDBe 4M55 · UniProt Q8NBZ7
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