MolNFT v1 · #14363 · protein
Crystal structure of the G359F (small subunit) point mutant of carbamoyl phosphate synthetase
1M6V · Carbamoyl phosphate synthetase large chain: “Crystal structure of the G359F (small subunit) point mutant of carbamoyl phosphate synthetase”. X-ray diffraction, 7 ligands (ADP, ORN, NET), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 1M6V
- Type
- protein
- Length
- 5,736 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 0.84
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 | 1059 | 40% helix, 20% strand | P00968 |
| B, D, F, H | Carbamoyl-phosphate synthetase small chain (EC 6.3.5.5) | protein | 375 | 25% 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 · 26 copies · chains A, B, C, D, E, F, G
- MN · Manganese (II) ion · metal · 12 copies · chains A, C, E, G
- CL · Chloride ion · ion · 28 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 | 989 | 0.84 | 0.85 | 76 | CL, ORN, NET |
| 2 | 982 | 0.83 | 0.84 | 76 | CL, ORN, NET |
| 3 | 889 | 0.82 | 0.84 | 95 | empty |
| 4 | 1026 | 0.82 | 0.83 | 72 | CL, ORN, NET |
| 5 | 1046 | 0.82 | 0.83 | 77 | CL, ORN, NET |
Interfaces
8 interfaces between chains.
- G–H · 2388 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2376 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2370 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2363 Ų buried · 40 hydrogen bonds · protein-protein
- C–E · 606 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1M6V · Crystal Structure of the G359F (small subunit) Point Mutant of Carbamoyl Phosphate… · the same entry in another collection · chain C against C, 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 1M6V · PDBe 1M6V · UniProt P00968 · UniProt P00907
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