Research workbench
Giardia lamblia prolyl-tRNA synthetase in complex with prolyl- adenylate
Analyse Giardia lamblia prolyl-tRNA synthetase in complex with prolyl- adenylate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IAL
- Type
- protein
- Length
- 1,001 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase
- EC
- 6.1.1.15
- UniProt
- A8BR89
- Ligands
- PR8
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase (EC 6.1.1.15) | protein | 496 | 39% helix, 27% strand | A8BR89 |
| B | Prolyl-tRNA synthetase (EC 6.1.1.15) | protein | 505 | 38% helix, 28% strand | A8BR89 |
Ligands and binding sites
- PR8 · 5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.80 | 0.96 | 32 | GOL |
| 2 | 444 | 0.72 | 0.82 | 44 | PR8, GOL |
| 3 | 450 | 0.71 | 0.82 | 42 | PR8, GOL |
| 4 | 429 | 0.58 | 0.74 | 35 | empty |
| 5 | 362 | 0.56 | 0.75 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2394 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3IAL · Giardia lamblia Prolyl-tRNA synthetase in complex with prolyl-adenylate · the same entry in another collection · chain B against B, 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 A8BR89
- Elsewhere: RCSB PDB 3IAL · PDBe 3IAL · UniProt A8BR89
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