Research workbench
Crystal structure of prolyl-tRNA synthetase from naegleria fowleri in complex with proline and adenosine monophophsphate (AMP)
Analyse Crystal structure of prolyl-tRNA synthetase from naegleria fowleri in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NAB
- Type
- protein
- Length
- 993 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase
- Ligands
- AMP, PRO, MG
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase | protein | 496 | 39% helix, 28% strand | — |
| B | Prolyl-tRNA synthetase | protein | 497 | 38% helix, 28% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- PRO · Proline · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.74 | 0.83 | 44 | empty |
| 2 | 407 | 0.73 | 0.84 | 43 | AMP, PRO, MG |
| 3 | 384 | 0.71 | 0.83 | 45 | AMP, PRO, MG |
| 4 | 399 | 0.58 | 0.75 | 38 | EDO |
| 5 | 153 | 0.56 | 0.82 | 24 | EDO |
Interfaces
1 interface between chains.
- A–B · 2109 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6NAB · Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with… · 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 6NAB · PDBe 6NAB
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