MolNFT v1 · #4876 · protein
Structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic archaeon pyrococcus furiosus bound to ADP
1E19: “Structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic archaeon…”. X-ray diffraction, 2 ligands (ADP, MG), 6 pockets (best druggability 0.66). MolNFT v1 #4876 on GenesisL1: 3D structure…
- PDB
- 1E19
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbamate kinase
- EC
- 2.7.2.2
- UniProt
- P95474
- Ligands
- ADP, MG
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbamate kinase (EC 2.7.2.2) | protein | 313 | 43% helix, 24% strand | P95474 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.66 | 0.76 | 71 | ADP, MG |
| 2 | 499 | 0.65 | 0.77 | 66 | ADP, MG |
| 3 | 124 | 0.58 | 0.84 | 20 | empty |
| 4 | 137 | 0.57 | 0.83 | 22 | empty |
| 5 | 82 | 0.42 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2507 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1E19 · Structure of the carbamate kinase-like carbamoyl phosphate synthetase from the… · the same entry in another collection · chain A against A, TM-score 1.00
- P95474 · AlphaFold monomer V2.0 prediction for carbamate kinase (P95474) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P95474
- Elsewhere: RCSB PDB 1E19 · PDBe 1E19 · UniProt P95474
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