MolNFT v1 · #160647 · protein
Crystal structure of asparagine-tRNA ligase from elizabethkingia sp. ccug 26117
6PQH · Asparagine--tRNA ligase: “Crystal structure of asparagine-tRNA ligase from elizabethkingia sp. ccug 26117”. X-ray diffraction, 20 pockets (best druggability 0.71). MolNFT v1 #160647 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PQH
- Type
- protein
- Length
- 1,899 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asparagine--tRNA ligase
- EC
- 6.1.1.22
- UniProt
- X5KA67
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Asparagine--tRNA ligase (EC 6.1.1.22) | protein | 472 | 38% helix, 24% strand | X5KA67 |
| B | Asparagine--tRNA ligase (EC 6.1.1.22) | protein | 479 | 37% helix, 24% strand | X5KA67 |
| C | Asparagine--tRNA ligase (EC 6.1.1.22) | protein | 471 | 37% helix, 24% strand | X5KA67 |
| D | Asparagine--tRNA ligase (EC 6.1.1.22) | protein | 477 | 37% helix, 24% strand | X5KA67 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.71 | 0.77 | 63 | empty |
| 2 | 677 | 0.70 | 0.78 | 65 | empty |
| 3 | 688 | 0.70 | 0.77 | 64 | empty |
| 4 | 660 | 0.69 | 0.77 | 60 | empty |
| 5 | 222 | 0.61 | 0.81 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 5104 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 5019 Ų buried · 75 hydrogen bonds · protein-protein
- A–D · 132 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PQH · Crystal structure of Asparagine-tRNA ligase from Elizabethkingia sp. CCUG 26117 · 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 X5KA67
- Elsewhere: RCSB PDB 6PQH · PDBe 6PQH · UniProt X5KA67
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