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Crystal structure of prolyl-tRNA synthetase from methanothermobacter thermautotrophicus

Analyse Crystal structure of prolyl-tRNA synthetase from methanothermobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NJ2
Type: protein
Length: 452 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proline-tRNA synthetase
EC: 6.1.1.15
UniProt: O26708
Ligands: ZN, MG
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proline-tRNA synthetase (EC 6.1.1.15)	protein	452	36% helix, 28% strand	O26708

Ligands and binding sites

ZN · Zinc ion · metal · chains A
MG · Magnesium ion · metal · 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	412	0.68	0.80	47	empty
2	109	0.42	0.77	27	empty
3	72	0.29	0.73	11	empty

Compared structures

1NJ2 · Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus · the same entry in another collection · chain A against A, TM-score 1.00
O26708 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (O26708) · a predicted model of the same protein · chain A against A, TM-score 0.99

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O26708
Elsewhere: RCSB PDB 1NJ2 · PDBe 1NJ2 · UniProt O26708

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