MolNFT v1 · #142663 · protein
Crystal structure of methanosarcina mazei PYLRS(Y306A/Y384F) complexed with ptmdzlys
6ABM · Pyrrolysine--tRNA ligase: “Crystal structure of methanosarcina mazei PYLRS(Y306A/Y384F) complexed with ptmdzlys”. X-ray diffraction, 4 ligands (ATP, 9VR, MG), 3 pockets (best druggability 0.78). MolNFT v1 #142663 on GenesisL1: 3D…
- PDB
- 6ABM
- 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
- ATP, 9VR, MG, K
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 267 | 37% helix, 24% strand | Q8PWY1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 9VR · (2S)-2-azanyl-6-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]methoxycarbonylamino]hexanoic acid · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- K · Potassium ion · metal · 2 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 | 415 | 0.78 | 0.87 | 52 | MG, ATP, 9VR |
| 2 | 78 | 0.37 | 0.77 | 15 | empty |
| 3 | 70 | 0.33 | 0.75 | 16 | empty |
Compared structures
- 6ABM · Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with pTmdZLys · 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 6ABM · PDBe 6ABM · UniProt Q8PWY1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.