MolNFT v1 · #156260 · protein
Pylrs C-terminus domain mutant bound with 1-methyl-L-tryptophan and ampnp
6LYA · Pyrrolysine--tRNA ligase: “Pylrs C-terminus domain mutant bound with 1-methyl-L-tryptophan and ampnp”. X-ray diffraction, 3 ligands (ANP, EXL, MG), 3 pockets (best druggability 0.69). MolNFT v1 #156260 on GenesisL1: 3D structure…
- PDB
- 6LYA
- Type
- protein
- Length
- 261 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysine--tRNA ligase
- EC
- 6.1.1.26
- UniProt
- A0A0F8JXW8
- Ligands
- ANP, EXL, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 261 | 39% helix, 23% strand | A0A0F8JXW8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- EXL · 1-Methyl-L-tryptophan · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.69 | 0.80 | 40 | ANP, MG, EXL |
| 2 | 85 | 0.32 | 0.74 | 17 | empty |
| 3 | 53 | 0.29 | 0.75 | 13 | empty |
Compared structures
- 6LYA · PylRS C-terminus domain mutant bound with 1-Methyl-L-tryptophan and AMPNP · 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
- Every structure of UniProt A0A0F8JXW8
- Elsewhere: RCSB PDB 6LYA · PDBe 6LYA · UniProt A0A0F8JXW8
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