MolNFT v1 · #82561 · protein

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with boclys and amppnp (form 2)

3VQY · Pyrrolysine--tRNA ligase: “Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with boclys and amppnp…”. X-ray diffraction, 3 ligands (ANP, LBY, MG), 2 pockets (best druggability 0.70). MolNFT v1…

PDB: 3VQY
Type: protein
Length: 257 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyrrolysine--tRNA ligase
EC: 6.1.1.26
Ligands: ANP, LBY, MG
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyrrolysine--tRNA ligase (EC 6.1.1.26)	protein	257	40% helix, 23% strand	—

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
LBY · N~6~-(tert-butoxycarbonyl)-L-lysine · ligand · chains A
MG · Magnesium ion · metal · 2 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	384	0.70	0.82	42	ANP, LBY, MG
2	67	0.32	0.75	13	empty

Compared structures

3VQY · Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with… · 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
Elsewhere: RCSB PDB 3VQY · PDBe 3VQY

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.