Research workbench
Crystal structure of methanosarcina mazei PYLRS(Y306A/Y384F) complexed with metzlys
Analyse Crystal structure of methanosarcina mazei PYLRS(Y306A/Y384F) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AAN
- 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
- Q8PWY1
- Ligands
- ATP, 9TX, MG, K
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 261 | 36% helix, 25% strand | Q8PWY1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 9TX · N6-{[(3-ethynylphenyl)methoxy]carbonyl}-L-lysine · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- K · Potassium ion · metal · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 413 | 0.79 | 0.88 | 51 | MG, ATP, 9TX |
| 2 | 108 | 0.39 | 0.75 | 17 | empty |
| 3 | 56 | 0.34 | 0.78 | 13 | empty |
Compared structures
- 6AAN · Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with mEtZLys · 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 6AAN · PDBe 6AAN · UniProt Q8PWY1
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