Research workbench
Crystal structure of the uridine diphosphate N- acetylglucosamine pyrophosphorylase from trypanosoma brucei in complex with inhibitor
Analyse Crystal structure of the uridine diphosphate N- acetylglucosamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BQH
- Type
- protein
- Length
- 521 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine pyrophosphorylase
- EC
- 2.7.7.23
- UniProt
- Q386Q8
- Ligands
- 9VU, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) | protein | 521 | 41% helix, 20% strand | Q386Q8 |
Ligands and binding sites
- 9VU · (3S)-3-[2-(1,3-benzodioxol-5-yl)-2-oxidanylidene-ethyl]-4-bromanyl-5-methyl-3-oxidanyl-1H-indol-2-one · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.70 | 0.77 | 85 | empty |
| 2 | 454 | 0.70 | 0.80 | 41 | empty |
| 3 | 229 | 0.64 | 0.83 | 40 | 9VU |
| 4 | 286 | 0.55 | 0.76 | 33 | empty |
| 5 | 109 | 0.47 | 0.80 | 20 | empty |
Compared structures
- 4BQH · Crystal structure of the uridine diphosphate N-acetylglucosamine pyrophosphorylase from… · 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 Q386Q8
- Elsewhere: RCSB PDB 4BQH · PDBe 4BQH · UniProt Q386Q8
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