MolNFT v1 · #28507 · protein

Crystal structure of the catalytic fragment of alanyl-tRNA synthetase in complex with L-serine

1YGB: “Crystal structure of the catalytic fragment of alanyl-tRNA synthetase in complex with L-serine”. X-ray diffraction, 1 ligand (SER), 3 pockets (best druggability 0.69). MolNFT v1 #28507 on GenesisL1: 3D structure, binding sites and…

PDB: 1YGB
Type: protein
Length: 448 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alanyl-tRNA synthetase
EC: 6.1.1.7
UniProt: O67323
Ligands: SER
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alanyl-tRNA synthetase (EC 6.1.1.7)	protein	448	45% helix, 18% strand	O67323

Ligands and binding sites

SER · Serine · ligand · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	574	0.69	0.78	56	SER
2	180	0.52	0.78	28	empty
3	72	0.37	0.77	15	empty

Compared structures

1YGB · Crystal Structure of the catalytic fragment of alanyl-tRNA synthetase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
O67323 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase (O67323) · 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 O67323
Elsewhere: RCSB PDB 1YGB · PDBe 1YGB · UniProt O67323

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