Research workbench
Crystal structure of carbamoyl phosphate synthetase complexed at CYS269 in the small subunit with the tetrahedral mimic L-glutamate gamma-semialdehyde
Analyse Crystal structure of carbamoyl phosphate synthetase complexed at CYS269 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CS0
- 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 subunit; Carbamoyl phosphate synthetase: small…
- 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 · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Carbamoyl phosphate synthetase: large subunit (EC 6.3.5.5) | protein | 1058 | 41% helix, 21% strand | P00968 |
| B, D, F, H | Carbamoyl phosphate synthetase: small subunit (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 · 33 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 · 29 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 5 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 | 1104 | 0.83 | 0.84 | 88 | CL, ORN, NET |
| 2 | 1062 | 0.82 | 0.83 | 78 | CL, ORN, NET |
| 3 | 1094 | 0.82 | 0.83 | 79 | CL, ORN, NET |
| 4 | 1076 | 0.82 | 0.83 | 77 | CL, ORN, NET |
| 5 | 175 | 0.82 | 0.97 | 36 | K, PO4, ADP |
Interfaces
8 interfaces between chains.
- E–F · 2453 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2449 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2447 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 2436 Ų buried · 46 hydrogen bonds · protein-protein
- C–E · 605 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 1CS0 · Crystal structure of carbamoyl phosphate synthetase complexed at CYS269 in the small… · the same entry in another collection · chain D against D, 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 1CS0 · PDBe 1CS0 · UniProt P00968 · UniProt P00907
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