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Crystal structure of human prolyl-tRNA synthetase (apo form)

Analyse Crystal structure of human prolyl-tRNA synthetase (apo form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K86
Type: protein
Length: 488 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: Homo sapiens
Molecule: Proline--tRNA ligase
EC: 6.1.1.15
UniProt: P07814
Ligands: ZN
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · resolution 2.4 · 1 distinct chain · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proline--tRNA ligase (EC 6.1.1.15)	protein	488	34% helix, 27% strand	P07814

Ligands and binding sites

ZN · Zinc ion · metal · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	729	0.72	0.78	60	empty
2	60	0.47	0.84	12	empty
3	96	0.40	0.77	19	empty
4	56	0.28	0.74	17	empty

Compared structures

4K86 · Crystal structure of human prolyl-tRNA synthetase (apo form) · the same entry in another collection · chain A against A, TM-score 1.00
P07814 · AlphaFold monomer V2.0 prediction for bifunctional GLUTAMATE/PROLINE --tRNA ligase… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P07814
Elsewhere: RCSB PDB 4K86 · PDBe 4K86 · UniProt P07814

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