MolNFT v1 · #141922 · protein

Crystal structure of a bacterial prors with ligands

5ZNK · Proline--tRNA ligase: “Crystal structure of a bacterial prors with ligands”. X-ray diffraction, 3 ligands (ANP, 9G3, MG), 3 pockets (best druggability 0.73). MolNFT v1 #141922 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5ZNK
Type: protein
Length: 562 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proline--tRNA ligase
EC: 6.1.1.15
UniProt: A0A227M497
Ligands: ANP, 9G3, MG
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proline--tRNA ligase (EC 6.1.1.15)	protein	562	30% helix, 31% strand	A0A227M497

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
9G3 · 7-chloro-6-fluoro-3-{2-oxo-3-[(2S)-piperidin-2-yl]propyl}quinazolin-4(3H)-one · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
GOL · Glycerol · additive · 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	748	0.73	0.79	64	ANP, MG, GOL, 9G3
2	61	0.39	0.80	16	empty
3	71	0.38	0.78	18	empty

Compared structures

5ZNK · Crystal structure of a bacterial ProRS with ligands · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A227M497
Elsewhere: RCSB PDB 5ZNK · PDBe 5ZNK · UniProt A0A227M497

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