Research workbench

Pylrs C-terminus domain mutant bound with 3-(1-naphthyl)-L-alanine and ampnp

Analyse Pylrs C-terminus domain mutant bound with 3-(1-naphthyl)-L-alanine and ampnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LY6
Type: protein
Length: 259 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: ANP, ALN, MG
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyrrolysine--tRNA ligase (EC 6.1.1.26)	protein	259	39% helix, 23% strand	A0A0F8JXW8

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
ALN · Naphthalen-2-yl-3-alanine · 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

3 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	433	0.67	0.79	46	ANP, MG, ALN
2	88	0.33	0.73	17	empty
3	53	0.30	0.76	13	empty

Compared structures

6LY6 · PylRS C-terminus domain mutant bound with 3-(1-Naphthyl)-L-alanine and AMPNP · 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 6LY6 · PDBe 6LY6 · UniProt A0A0F8JXW8

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