MolNFT v1 · #141375 · protein

Crystal structure of the glycyl-tRNA synthetase (glyrs) in nanoarchaeum equitans

5Z5E · NEQ417: “Crystal structure of the glycyl-tRNA synthetase (glyrs) in nanoarchaeum equitans”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.80). MolNFT v1 #141375 on GenesisL1: 3D structure, binding sites and…

PDB: 5Z5E
Type: protein
Length: 911 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NEQ417
UniProt: Q74N31
Ligands: SO4
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NEQ417	protein	443	36% helix, 29% strand	Q74N31
B	NEQ417	protein	468	34% helix, 31% strand	Q74N31

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	703	0.80	0.84	68	empty
2	632	0.71	0.79	52	SO4
3	546	0.68	0.79	53	SO4
4	308	0.68	0.82	38	empty
5	346	0.67	0.81	34	empty

Interfaces

1 interface between chains.

A–B · 4276 Å² buried · 65 hydrogen bonds · protein-protein

Compared structures

5Z5E · Crystal structure of the Glycyl-tRNA synthetase (GlyRS) in Nanoarchaeum equitans · 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 Q74N31
Elsewhere: RCSB PDB 5Z5E · PDBe 5Z5E · UniProt Q74N31

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