Research workbench
Structure mmnags bound with L-arginine
Analyse Structure mmnags bound with L-arginine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KZT
- Type
- protein
- Length
- 1,724 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
- ARG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, X, Y | N-acetylglutamate kinase / N-acetylglutamate synthase (EC 2.3.1.1, 2.7.2.8) | protein | 431 | 37% helix, 23% strand | Q0ASS9 |
Ligands and binding sites
- ARG · Arginine · ligand · 4 copies · chains A, B, X, Y
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, X, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.75 | 0.96 | 22 | empty |
| 2 | 899 | 0.75 | 0.78 | 89 | ARG, PEG |
| 3 | 788 | 0.74 | 0.79 | 88 | ARG, PEG |
| 4 | 102 | 0.74 | 0.95 | 34 | empty |
| 5 | 784 | 0.73 | 0.78 | 90 | ARG, PEG |
Interfaces
4 interfaces between chains.
- B–Y · 1803 Ų buried · 15 hydrogen bonds · protein-protein
- A–X · 1756 Ų buried · 16 hydrogen bonds · protein-protein
- X–Y · 1097 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1094 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4KZT · Structure mmNAGS bound with L-arginine · 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 4KZT · PDBe 4KZT · UniProt Q0ASS9
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