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Structure and allosteric regulation of the uridine monophosphate kinase from mycobacterium tuberculosis
Analyse Structure and allosteric regulation of the uridine monophosphate kinase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NWY
- Type
- protein
- Length
- 1,364 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- P65929
- Ligands
- GTP, UDP
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.22) | protein | 227 | 39% helix, 19% strand | P65929 |
| B | Uridylate kinase (EC 2.7.4.22) | protein | 231 | 38% helix, 20% strand | P65929 |
| C | Uridylate kinase (EC 2.7.4.22) | protein | 230 | 39% helix, 20% strand | P65929 |
| D | Uridylate kinase (EC 2.7.4.22) | protein | 230 | 39% helix, 17% strand | P65929 |
| E | Uridylate kinase (EC 2.7.4.22) | protein | 220 | 42% helix, 17% strand | P65929 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 226 | 42% helix, 18% strand | P65929 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, D, B, C, E, F
- UDP · Uridine-5'-diphosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.77 | 0.85 | 61 | GTP |
| 2 | 252 | 0.71 | 0.86 | 30 | empty |
| 3 | 198 | 0.68 | 0.86 | 32 | empty |
| 4 | 161 | 0.66 | 0.87 | 25 | GTP |
| 5 | 322 | 0.65 | 0.80 | 55 | empty |
Interfaces
12 interfaces between chains.
- A–E · 1526 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1443 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1328 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 885 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 862 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3NWY · Structure and allosteric regulation of the uridine monophosphate kinase 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 P65929
- Elsewhere: RCSB PDB 3NWY · PDBe 3NWY · UniProt P65929
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