MolNFT v1 · #77646 · protein
Crystal structure of the archaeal asparagine synthetase a complexed with L-asparagine and adenosine monophosphate
3RL6: “Crystal structure of the archaeal asparagine synthetase a complexed with L-asparagine and adenosine…”. X-ray diffraction, 3 ligands (ASN, AMP, MG), 4 pockets (best druggability 0.80). MolNFT v1 #77646 on GenesisL1: 3D structure…
- PDB
- 3RL6
- Type
- protein
- Length
- 579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Archaeal asparagine synthetase a
- UniProt
- Q9V228
- Ligands
- ASN, AMP, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Archaeal asparagine synthetase a | protein | 294 | 37% helix, 23% strand | Q9V228 |
| B | Archaeal asparagine synthetase a | protein | 285 | 38% helix, 24% strand | Q9V228 |
Ligands and binding sites
- ASN · Asparagine · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.80 | 0.90 | 52 | ASN, AMP, MG |
| 2 | 442 | 0.71 | 0.82 | 53 | ASN, AMP |
| 3 | 81 | 0.38 | 0.77 | 15 | empty |
| 4 | 65 | 0.34 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2970 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3RL6 · Crystal structure of the archaeal asparagine synthetase A complexed with L-Asparagine and… · 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 Q9V228
- Elsewhere: RCSB PDB 3RL6 · PDBe 3RL6 · UniProt Q9V228
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