Research workbench
Crystal structure of a putative aspartyl-tRNA synthetase from leishmania major friedlin
Analyse Crystal structure of a putative aspartyl-tRNA synthetase from leishmania major… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OD8
- Type
- protein
- Length
- 1,011 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aspartyl-tRNA synthetase
- EC
- 6.1.1.12
- UniProt
- Q4Q7R2
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aspartyl-tRNA synthetase (EC 6.1.1.12) | protein | 506 | 32% helix, 27% strand | Q4Q7R2 |
| B | Putative aspartyl-tRNA synthetase (EC 6.1.1.12) | protein | 505 | 32% helix, 27% strand | Q4Q7R2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.72 | 0.79 | 75 | EDO, FMT |
| 2 | 556 | 0.71 | 0.80 | 71 | EDO, FMT |
| 3 | 534 | 0.70 | 0.80 | 58 | empty |
| 4 | 450 | 0.69 | 0.80 | 65 | EDO |
| 5 | 173 | 0.51 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 5051 Ų buried · 102 hydrogen bonds · protein-protein
Compared structures
- 6OD8 · Crystal structure of a putative aspartyl-tRNA synthetase from Leishmania major Friedlin · 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 Q4Q7R2
- Elsewhere: RCSB PDB 6OD8 · PDBe 6OD8 · UniProt Q4Q7R2
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