MolNFT v1 · #12355 · protein
Inactivation of the amidotransferase activity of carbamoyl phosphate synthetase by the antibiotic acivicin
1KEE · Carbamoyl-phosphate synthetase large chain: “Inactivation of the amidotransferase activity of carbamoyl phosphate synthetase by the antibiotic acivicin”. X-ray diffraction, 7 ligands (ADP, ORN, NET), 20 pockets (best druggability…
- PDB
- 1KEE
- Type
- protein
- Length
- 5,748 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbamoyl-phosphate synthetase large chain; Carbamoyl-phosphate synthetase small chain
- EC
- 6.3.5.5
- UniProt
- P00968, P00907
- Ligands
- ADP, ORN, NET, K, MN, CL, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Carbamoyl-phosphate synthetase large chain (EC 6.3.5.5) | protein | 1058 | 40% helix, 20% strand | P00968 |
| B, D, F, H | Carbamoyl-phosphate synthetase small chain (EC 6.3.5.5) | protein | 379 | 26% helix, 32% strand | P00907 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, C, E, G
- ORN · L-ornithine · ligand · 4 copies · chains A, C, E, G
- NET · Tetraethylammonium ion · ligand · 4 copies · chains A, C, E, G
- K · Potassium ion · metal · 32 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 12 copies · chains A, C, E, G
- CL · Chloride ion · ion · 22 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.83 | 0.84 | 82 | CL, ORN, NET |
| 2 | 968 | 0.83 | 0.84 | 70 | CL, ORN, NET |
| 3 | 1080 | 0.82 | 0.83 | 72 | CL, ORN, NET |
| 4 | 1079 | 0.82 | 0.83 | 74 | CL, ORN, NET |
| 5 | 179 | 0.82 | 0.97 | 37 | MN, PO4, ADP |
Interfaces
8 interfaces between chains.
- E–F · 2473 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 2464 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2462 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2462 Ų buried · 43 hydrogen bonds · protein-protein
- A–G · 594 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 1KEE · Inactivation of the Amidotransferase Activity of Carbamoyl Phosphate Synthetase by the… · the same entry in another collection · chain G against G, TM-score 1.00
- P00968 · AlphaFold monomer V2.0 prediction for carbamoyl-phosphate synthase large chain (P00968) · a predicted model of the same protein · chain G 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 P00968
- Every structure of UniProt P00907
- Elsewhere: RCSB PDB 1KEE · PDBe 1KEE · UniProt P00968 · UniProt P00907
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