MolNFT v1 · #143507 · protein

Crystal structure of glutamate-tRNA synthetase from helicobacter pylori

6B1P · Glutamate--tRNA ligase 1: “Crystal structure of glutamate-tRNA synthetase from helicobacter pylori”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #143507 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6B1P
Type: protein
Length: 430 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate--tRNA ligase 1
EC: 6.1.1.17
UniProt: B5Z6J9
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate--tRNA ligase 1 (EC 6.1.1.17)	protein	430	47% helix, 12% strand	B5Z6J9

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	263	0.69	0.84	35	empty
2	123	0.50	0.80	21	empty
3	98	0.42	0.78	19	empty
4	52	0.34	0.78	18	empty

Compared structures

6B1P · Crystal Structure of Glutamate-tRNA Synthetase from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
B5Z6J9 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase 1 (B5Z6J9) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 B5Z6J9
Elsewhere: RCSB PDB 6B1P · PDBe 6B1P · UniProt B5Z6J9

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