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The crystal structure of aaleurs-CP1

Analyse The crystal structure of aaleurs-CP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PZ0
Type: protein
Length: 844 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucyl-tRNA synthetase subunit alpha
EC: 6.1.1.4
UniProt: O66680
Ligands: CA
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Leucyl-tRNA synthetase subunit alpha (EC 6.1.1.4)	protein	211	37% helix, 23% strand	O66680

Ligands and binding sites

CA · Calcium ion · metal · chains B

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	626	0.64	0.74	59	empty
2	138	0.55	0.82	21	empty
3	122	0.54	0.82	20	empty
4	118	0.53	0.82	21	empty
5	160	0.52	0.79	19	empty

Interfaces

3 interfaces between chains.

A–D · 209 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 208 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 126 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3PZ0 · The crystal structure of AaLeuRS-CP1 · the same entry in another collection · chain A against A, TM-score 1.00
O66680 · AlphaFold monomer V2.0 prediction for leucine--tRNA ligase subunit alpha (O66680) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O66680
Elsewhere: RCSB PDB 3PZ0 · PDBe 3PZ0 · UniProt O66680

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