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Crystal structure of human carbamoyl phosphate synthetase I (CPS1), ligand-bound form
Analyse Crystal structure of human carbamoyl phosphate synthetase I (CPS1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DOU
- Type
- protein
- Length
- 5,699 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbamoyl-phosphate synthase [ammonia], mitochondrial
- EC
- 6.3.4.16
- UniProt
- P31327
- Ligands
- ADP, NLG, K, MG, NI, PO4, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 1422 | 33% helix, 23% strand | P31327 |
| B | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 1426 | 34% helix, 23% strand | P31327 |
| C | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 1421 | 33% helix, 24% strand | P31327 |
| D | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 1430 | 34% helix, 23% strand | P31327 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D
- NLG · N-acetyl-L-glutamate · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 18 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · chains A
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 | 888 | 0.82 | 0.84 | 110 | ADP, MG |
| 2 | 545 | 0.82 | 0.88 | 79 | empty |
| 3 | 1114 | 0.81 | 0.83 | 121 | ADP, MG, CL |
| 4 | 1079 | 0.81 | 0.82 | 112 | ADP, MG, CL |
| 5 | 960 | 0.81 | 0.82 | 65 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1186 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1171 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 289 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DOU · Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), ligand-bound form · the same entry in another collection · chain D against D, TM-score 1.00
- P31327 · AlphaFold monomer V2.0 prediction for carbamoyl-phosphate synthase [ammonia]… · a predicted model of the same protein · 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 P31327
- Elsewhere: RCSB PDB 5DOU · PDBe 5DOU · UniProt P31327
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