MolNFT v1 · #116797 · protein
Crystal structure of human carbamoyl phosphate synthetase I (CPS1), apo form
5DOT · Carbamoyl-phosphate synthase [ammonia], mitochondrial: “Crystal structure of human carbamoyl phosphate synthetase I (CPS1), apo form”. X-ray diffraction, 1 ligand (NI), 20 pockets (best druggability 0.85). MolNFT v1 #116797 on…
- PDB
- 5DOT
- Type
- protein
- Length
- 2,703 residues
- Chains
- 2
- 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
- NI
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 1352 | 32% helix, 24% strand | P31327 |
| B | Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) | protein | 1351 | 33% helix, 24% strand | P31327 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
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 | 1120 | 0.85 | 0.86 | 114 | empty |
| 2 | 851 | 0.84 | 0.86 | 86 | empty |
| 3 | 307 | 0.83 | 0.94 | 38 | empty |
| 4 | 304 | 0.83 | 0.94 | 36 | empty |
| 5 | 498 | 0.80 | 0.87 | 65 | empty |
Interfaces
1 interface between chains.
- A–B · 1419 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5DOT · Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form · the same entry in another collection · chain A against A, TM-score 1.00
- P31327 · AlphaFold monomer V2.0 prediction for carbamoyl-phosphate synthase [ammonia]… · 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 P31327
- Elsewhere: RCSB PDB 5DOT · PDBe 5DOT · UniProt P31327
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.