MolNFT v1 · #104300 · protein
Crystal structure of the C-terminal domain of ackrs-1 bound with N- acetyl-lysine and adpnp
4Q6G · Pyrrolysine--tRNA ligase: “Crystal structure of the C-terminal domain of ackrs-1 bound with N- acetyl-lysine and adpnp”. X-ray diffraction, 2 ligands (ANP, ALY), 2 pockets (best druggability 0.74). MolNFT v1 #104300 on GenesisL1: 3D…
- PDB
- 4Q6G
- Type
- protein
- Length
- 267 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
- Q8PWY1
- Ligands
- ANP, ALY
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 267 | 38% helix, 24% strand | Q8PWY1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- ALY · N(6)-acetyllysine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.74 | 0.85 | 45 | ANP, ALY |
| 2 | 103 | 0.36 | 0.74 | 19 | empty |
Compared structures
- 4Q6G · Crystal Structure of the C-terminal domain of AcKRS-1 bound with N-acetyl-lysine and ADPNP · 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 0.99
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 4Q6G · PDBe 4Q6G · UniProt Q8PWY1
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