Research workbench
Protein structure of usp from L. major bound to uridine-5'-diphosphate -arabinose
Analyse Protein structure of usp from L. major bound to uridine-5'-diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OH3
- Type
- protein
- Length
- 585 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
- UAD
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-sugar pyrophosphorylase (EC 2.7.7.64) | protein | 585 | 32% helix, 23% strand | D3G6S4 |
Ligands and binding sites
- UAD · [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2S,3R,4S,5S)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate · 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 | 996 | 0.77 | 0.79 | 69 | UAD |
| 2 | 283 | 0.71 | 0.85 | 38 | empty |
| 3 | 103 | 0.51 | 0.82 | 23 | empty |
| 4 | 230 | 0.48 | 0.74 | 27 | empty |
| 5 | 85 | 0.35 | 0.75 | 17 | empty |
Compared structures
- 3OH3 · Protein structure of USP from L. major bound to URIDINE-5'-DIPHOSPHATE -Arabinose · 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 3OH3 · PDBe 3OH3 · UniProt D3G6S4
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