MolNFT v1 · #136890 · protein + RNA
Crystal structure of the tRNA binding domain of pyrrolysyl-tRNA synthetase mutant (32A ntd) bound to TRNA(PYL)
5V6X · Pyrrolysine--tRNA ligase: “Crystal structure of the tRNA binding domain of pyrrolysyl-tRNA synthetase mutant (32A ntd) bound to TRNA(PYL)”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.78). MolNFT v1 #136890 on…
- PDB
- 5V6X
- Type
- protein + RNA
- Length
- 310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysine--tRNA ligase; RNA (70-mer)
- EC
- 6.1.1.26
- UniProt
- Q8PWY1
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 84 | 26% helix, 32% strand | Q8PWY1 |
| C | RNA (70-mer) | rna | 70 | — | — |
| D | RNA (70-mer) | rna | 72 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.78 | 0.84 | 53 | empty |
| 2 | 567 | 0.76 | 0.84 | 41 | empty |
| 3 | 441 | 0.61 | 0.76 | 42 | empty |
| 4 | 472 | 0.60 | 0.76 | 33 | empty |
| 5 | 292 | 0.55 | 0.77 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1101 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–C · 1057 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–D · 316 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 307 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5V6X · Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase mutant (32A… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PWY1 · AlphaFold monomer V2.0 prediction for pyrrolysine--tRNA ligase (Q8PWY1) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q8PWY1
- Elsewhere: RCSB PDB 5V6X · PDBe 5V6X · UniProt Q8PWY1
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