Research workbench
Crystal structure of cytoplasmic serine-tRNA ligase from naegleria fowleri in complex with AMP
Analyse Crystal structure of cytoplasmic serine-tRNA ligase from naegleria fowleri in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BLJ
- Type
- protein
- Length
- 1,339 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine-tRNA ligase
- Ligands
- AMP
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine-tRNA ligase | protein | 473 | 44% helix, 19% strand | — |
| B | Serine-tRNA ligase | protein | 435 | 44% helix, 20% strand | — |
| C | Serine-tRNA ligase | protein | 431 | 43% helix, 21% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.80 | 0.82 | 95 | AMP |
| 2 | 587 | 0.77 | 0.84 | 56 | AMP |
| 3 | 573 | 0.71 | 0.80 | 55 | AMP |
| 4 | 393 | 0.70 | 0.82 | 49 | empty |
| 5 | 166 | 0.64 | 0.85 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2582 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 289 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6BLJ · Crystal structure of cytoplasmic Serine-tRNA ligase from Naegleria fowleri in complex… · 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
- Elsewhere: RCSB PDB 6BLJ · PDBe 6BLJ
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