Research workbench
Crystal structure of uridylate kinase from helicobacter pylori
Analyse Crystal structure of uridylate kinase from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A7W
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- P56106
- Ligands
- GTP
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate kinase (EC 2.7.4.22) | protein | 226 | 39% helix, 19% strand | P56106 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.52 | 0.84 | 18 | empty |
| 2 | 131 | 0.49 | 0.79 | 29 | GOL |
| 3 | 120 | 0.48 | 0.80 | 30 | GOL |
| 4 | 94 | 0.36 | 0.75 | 17 | empty |
| 5 | 76 | 0.35 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1333 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 P56106
- Elsewhere: RCSB PDB 4A7W · PDBe 4A7W · UniProt P56106
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