MolNFT v1 · #20805 · protein

Methionyl-tRNA synthetase from pyrococcus abyssi

1RQG: “Methionyl-tRNA synthetase from pyrococcus abyssi”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.74). MolNFT v1 #20805 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1RQG
Type: protein
Length: 606 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionyl-tRNA synthetase
EC: 6.1.1.10
UniProt: Q9V011
Ligands: ZN
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionyl-tRNA synthetase (EC 6.1.1.10)	protein	606	49% helix, 14% strand	Q9V011

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	836	0.74	0.78	60	empty
2	158	0.58	0.82	25	empty
3	158	0.54	0.80	24	empty
4	108	0.37	0.74	23	empty

Compared structures

1RQG · Methionyl-tRNA synthetase from Pyrococcus abyssi · the same entry in another collection · chain A against A, TM-score 1.00
Q9V011 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase (Q9V011) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9V011
Elsewhere: RCSB PDB 1RQG · PDBe 1RQG · UniProt Q9V011

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