Research workbench
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in triclinic crystal form
Analyse Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VQX
- Type
- protein
- Length
- 1,010 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysine--tRNA ligase
- EC
- 6.1.1.26
- Ligands
- AMP, BLK, PO4
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 253 | 37% helix, 26% strand | — |
| B | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 246 | 40% helix, 23% strand | — |
| C | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 254 | 38% helix, 23% strand | — |
| D | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 257 | 37% helix, 25% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- BLK · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-6-[(2-methylpropan-2-yl)oxycarbonylamino]hexanoate · ligand · 2 copies · chains C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.75 | 0.83 | 49 | AMP |
| 2 | 422 | 0.68 | 0.80 | 47 | BLK |
| 3 | 394 | 0.68 | 0.80 | 41 | BLK |
| 4 | 316 | 0.67 | 0.82 | 38 | AMP |
| 5 | 169 | 0.51 | 0.78 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2435 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2421 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3VQX · Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in triclinic… · 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 3VQX · PDBe 3VQX
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