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Crystal structure of the semet substituted catalytic domain of pyrrolysyl-tRNA synthetase

Analyse Crystal structure of the semet substituted catalytic domain of pyrrolysyl-tRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VQW
Type: protein
Length: 258 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, MG
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyrrolysine--tRNA ligase (EC 6.1.1.26)	protein	258	38% helix, 23% strand	—

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · 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	413	0.69	0.81	44	ANP, MG
2	86	0.33	0.74	14	empty
3	60	0.30	0.75	13	empty

Modifications

Observed in the structure: 5 modified (engineered).

Compared structures

3VQW · Crystal structure of the SeMet substituted catalytic domain of pyrrolysyl-tRNA synthetase · 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 3VQW · PDBe 3VQW

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