MolNFT v1 · #71122 · protein
Entamoeba histolytica asparaginyl-tRNA synthetase (asnrs) in complex with asparaginyl-adenylate
3M4P · Asparaginyl-tRNA synthetase, putative: “Entamoeba histolytica asparaginyl-tRNA synthetase (asnrs) in complex with asparaginyl-adenylate”. X-ray diffraction, 2 ligands (4AD, SO4), 18 pockets (best druggability 0.73). MolNFT v1 #71122…
- PDB
- 3M4P
- Type
- protein
- Length
- 1,734 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asparaginyl-tRNA synthetase, putative
- EC
- 6.1.1.22
- UniProt
- C4LWW8
- Ligands
- 4AD, SO4
- Pockets
- 18 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Asparaginyl-tRNA synthetase, putative (EC 6.1.1.22) | protein | 435 | 31% helix, 28% strand | C4LWW8 |
| B, D | Asparaginyl-tRNA synthetase, putative (EC 6.1.1.22) | protein | 435 | 32% helix, 29% strand | C4LWW8 |
| C | Asparaginyl-tRNA synthetase, putative (EC 6.1.1.22) | protein | 429 | 32% helix, 29% strand | C4LWW8 |
Ligands and binding sites
- 4AD · 4-amino-1,4-dioxobutan-2-aminium adenosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.73 | 0.79 | 83 | 4AD |
| 2 | 640 | 0.73 | 0.80 | 68 | 4AD |
| 3 | 696 | 0.73 | 0.79 | 63 | 4AD |
| 4 | 663 | 0.71 | 0.78 | 56 | 4AD |
| 5 | 427 | 0.66 | 0.79 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4184 Ų buried · 74 hydrogen bonds · protein-protein
- C–D · 4121 Ų buried · 75 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3M4P · Entamoeba histolytica asparaginyl-tRNA synthetase (AsnRS) in complex with… · the same entry in another collection · chain C against C, 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 C4LWW8
- Elsewhere: RCSB PDB 3M4P · PDBe 3M4P · UniProt C4LWW8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.