MolNFT v1 · #135911 · protein + RNA
Crystal structure of the tRNA binding domain of pyrrolysyl-tRNA synthetase bound to TRNA(PYL)
5UD5 · Pyrrolysine--tRNA ligase: “Crystal structure of the tRNA binding domain of pyrrolysyl-tRNA synthetase bound to TRNA(PYL)”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.75). MolNFT v1 #135911 on GenesisL1: 3D…
- PDB
- 5UD5
- Type
- protein + RNA
- Length
- 314 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
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 86 | 27% helix, 31% 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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.75 | 0.79 | 66 | empty |
| 2 | 800 | 0.75 | 0.80 | 43 | empty |
| 3 | 135 | 0.63 | 0.87 | 27 | empty |
| 4 | 140 | 0.61 | 0.85 | 26 | empty |
| 5 | 358 | 0.59 | 0.77 | 35 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1240 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–C · 1199 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–D · 333 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 329 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 94 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5UD5 · Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to… · 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 0.95
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 5UD5 · PDBe 5UD5 · UniProt Q8PWY1
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