MolNFT v1 · #73923 · protein
Protein structure of usp from L. major bound to uridine-5'- diphosphate-galacturonic acid
3OH1 · Udp-sugar pyrophosphorylase: “Protein structure of usp from L. major bound to uridine-5'- diphosphate-galacturonic acid”. X-ray diffraction, 1 ligand (UGB), 5 pockets (best druggability 0.72). MolNFT v1 #73923 on GenesisL1: 3D…
- PDB
- 3OH1
- Type
- protein
- Length
- 582 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-sugar pyrophosphorylase
- EC
- 2.7.7.64
- UniProt
- D3G6S4
- Ligands
- UGB
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-sugar pyrophosphorylase (EC 2.7.7.64) | protein | 582 | 33% helix, 23% strand | D3G6S4 |
Ligands and binding sites
- UGB · (2S,3R,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4,5-trihydroxy-oxane-2-carboxylic acid · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.72 | 0.77 | 71 | UGB |
| 2 | 269 | 0.70 | 0.85 | 36 | GOL |
| 3 | 110 | 0.50 | 0.81 | 23 | empty |
| 4 | 237 | 0.48 | 0.74 | 28 | empty |
| 5 | 77 | 0.31 | 0.74 | 15 | empty |
Compared structures
- 3OH1 · Protein structure of USP from L. major bound to URIDINE-5'-DIPHOSPHATE-Galacturonic acid · 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 D3G6S4
- Elsewhere: RCSB PDB 3OH1 · PDBe 3OH1 · UniProt D3G6S4
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