MolNFT v1 · #142650 · protein
Crystal structure of methanosarcina mazei PYLRS(Y306A/Y384F) complexed with pampylys
6AB0 · Pyrrolysine--tRNA ligase: “Crystal structure of methanosarcina mazei PYLRS(Y306A/Y384F) complexed with pampylys”. X-ray diffraction, 5 ligands (ATP, 9UF, MG), 3 pockets (best druggability 0.80). MolNFT v1 #142650 on GenesisL1: 3D…
- PDB
- 6AB0
- Type
- protein
- Length
- 264 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
- ATP, 9UF, MG, K, PO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 264 | 38% helix, 25% strand | A0A0F8JXW8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 9UF · N6-{[(6-aminopyridin-3-yl)methoxy]carbonyl}-L-lysine · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- K · Potassium ion · metal · 3 copies · chains A
- PO4 · Phosphate ion · ion · 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 | 415 | 0.80 | 0.88 | 55 | MG, ATP, 9UF |
| 2 | 97 | 0.38 | 0.76 | 16 | empty |
| 3 | 71 | 0.35 | 0.77 | 14 | K |
Compared structures
- 6AB0 · Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with pAmPyLys · 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 6AB0 · PDBe 6AB0 · UniProt A0A0F8JXW8
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