Research workbench
Cryoem structure of mycobacterium tuberculosis ump kinase (umpk) in complex with udp and UTP
Analyse Cryoem structure of mycobacterium tuberculosis ump kinase (umpk) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BES
- Type
- protein
- Length
- 617 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- A0A045IH65
- Ligands
- UDP, UTP
- Pockets
- 8 · best druggability 0.65
Structure
electron microscopy · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate kinase (EC 2.7.4.22) | protein | 229 | 42% helix, 19% strand | A0A045IH65 |
| C | Uridylate kinase (EC 2.7.4.22) | protein | 159 | 45% helix, 18% strand | A0A045IH65 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.65 | 0.79 | 58 | UDP |
| 2 | 321 | 0.64 | 0.80 | 35 | UTP |
| 3 | 346 | 0.62 | 0.79 | 44 | UDP |
| 4 | 192 | 0.62 | 0.83 | 27 | empty |
| 5 | 165 | 0.57 | 0.82 | 32 | UDP |
Interfaces
3 interfaces between chains.
- B–C · 1412 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 871 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 218 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7BES · CryoEM structure of Mycobacterium tuberculosis UMP Kinase (UMPK) in complex with UDP and… · 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 A0A045IH65
- Elsewhere: RCSB PDB 7BES · PDBe 7BES · UniProt A0A045IH65
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