Research workbench
Crystal structure of the G359F (small subunit) point mutant of carbamoyl phosphate synthetase
Analyse Crystal structure of the G359F (small subunit) point mutant of carbamoyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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