Research workbench
Crystal structures of seleno-substituted mutant mmnags in space group P212121
Analyse Crystal structures of seleno-substituted mutant mmnags in space group P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S6G
- Type
- protein
- Length
- 1,714 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglutamate kinase / N-acetylglutamate synthase
- EC
- 2.3.1.1, 2.7.2.8
- UniProt
- Q0ASS9
- Ligands
- COA, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglutamate kinase / N-acetylglutamate synthase (EC 2.3.1.1, 2.7.2.8) | protein | 436 | 43% helix, 23% strand | Q0ASS9 |
| B, X | N-acetylglutamate kinase / N-acetylglutamate synthase (EC 2.3.1.1, 2.7.2.8) | protein | 435 | 40% helix, 23% strand | Q0ASS9 |
| Y | N-acetylglutamate kinase / N-acetylglutamate synthase (EC 2.3.1.1, 2.7.2.8) | protein | 408 | 37% helix, 21% strand | Q0ASS9 |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains B, Y
- SO4 · Sulfate ion · ion · chains X
- MLI · Malonate ion · additive · 2 copies · chains A, X, Y
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.78 | 0.86 | 60 | empty |
| 2 | 241 | 0.76 | 0.90 | 41 | empty |
| 3 | 211 | 0.76 | 0.91 | 41 | empty |
| 4 | 815 | 0.75 | 0.80 | 78 | MLI, EDO |
| 5 | 781 | 0.75 | 0.80 | 80 | empty |
Interfaces
5 interfaces between chains.
- A–X · 1682 Ų buried · 14 hydrogen bonds · protein-protein
- B–Y · 1233 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1011 Ų buried · 20 hydrogen bonds · protein-protein
- X–Y · 979 Ų buried · 17 hydrogen bonds · protein-protein
- B–X · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3S6G · Crystal structures of Seleno-substituted mutant mmNAGS in space group P212121 · the same entry in another collection · 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 Q0ASS9
- Elsewhere: RCSB PDB 3S6G · PDBe 3S6G · UniProt Q0ASS9
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