MolNFT v1 · #173911 · protein
Cryoem structure of mycobacterium tuberculosis ump kinase (umpk) in complex with udp and UTP
7BES · Uridylate kinase: “Cryoem structure of mycobacterium tuberculosis ump kinase (umpk) in complex with udp and UTP”. Electron microscopy, 2 ligands (UDP, UTP), 8 pockets (best druggability 0.65). MolNFT v1 #173911 on GenesisL1: 3D…
- 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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