MolNFT v1 · #168703 · protein
Crystal structure of aspartyl-tRNA ligase from elizabethkingia sp.
6WOM · Aspartate--tRNA ligase: “Crystal structure of aspartyl-tRNA ligase from elizabethkingia sp.”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.86). MolNFT v1 #168703 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WOM
- Type
- protein
- Length
- 1,715 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate--tRNA ligase
- EC
- 6.1.1.12
- UniProt
- A0A1T3DDI2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate--tRNA ligase (EC 6.1.1.12) | protein | 583 | 32% helix, 26% strand | A0A1T3DDI2 |
| C | Aspartate--tRNA ligase (EC 6.1.1.12) | protein | 549 | 33% helix, 25% strand | A0A1T3DDI2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.86 | 0.96 | 66 | empty |
| 2 | 926 | 0.74 | 0.78 | 90 | empty |
| 3 | 922 | 0.74 | 0.78 | 77 | empty |
| 4 | 823 | 0.72 | 0.77 | 75 | empty |
| 5 | 191 | 0.70 | 0.88 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5532 Ų buried · 104 hydrogen bonds · protein-protein
- B–C · 166 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WOM · Crystal structure of Aspartyl-tRNA ligase from Elizabethkingia sp. · 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 A0A1T3DDI2
- Elsewhere: RCSB PDB 6WOM · PDBe 6WOM · UniProt A0A1T3DDI2
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