MolNFT v1 · #85291 · protein
Crystal structure of uridylate kinase from helicobacter pylori
4A7X: “Crystal structure of uridylate kinase from helicobacter pylori”. X-ray diffraction, 1 ligand (UDP), 20 pockets (best druggability 0.77). MolNFT v1 #85291 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4A7X
- Type
- protein
- Length
- 1,381 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- P56106
- Ligands
- UDP
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uridylate kinase (EC 2.7.4.22) | protein | 234 | 39% helix, 19% strand | P56106 |
| B, D | Uridylate kinase (EC 2.7.4.22) | protein | 228 | 41% helix, 19% strand | P56106 |
| E | Uridylate kinase (EC 2.7.4.22) | protein | 227 | 40% helix, 19% strand | P56106 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 230 | 38% helix, 20% strand | P56106 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.77 | 0.80 | 86 | empty |
| 2 | 120 | 0.76 | 0.96 | 29 | empty |
| 3 | 856 | 0.76 | 0.80 | 62 | empty |
| 4 | 119 | 0.74 | 0.95 | 29 | empty |
| 5 | 486 | 0.68 | 0.79 | 60 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1538 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1522 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1471 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 947 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 939 Ų buried · 7 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 4A7X · PDBe 4A7X · UniProt P56106
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.