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Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-Sulfamoyl)uridine

Analyse Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HI0
Type: protein
Length: 428 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.25
Source: Klebsiella pneumoniae
Molecule: Serine--tRNA ligase
EC: 6.1.1.11
UniProt: W9BNU9
Ligands: FZK, CA
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · resolution 2.25 · 1 distinct chain · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serine--tRNA ligase (EC 6.1.1.11)	protein	428	43% helix, 20% strand	W9BNU9

Ligands and binding sites

FZK · 5'-O-(N-(L-seryl)-Sulfamoyl)uridine · ligand · chains A
CA · Calcium ion · metal · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 3 copies · 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	684	0.74	0.80	61	EDO, FZK, CA
2	151	0.53	0.80	22	empty
3	70	0.36	0.77	14	empty

Compared structures

6HI0 · Klebsiella pneumoniae seryl-tRNA synthetase in complex with 5'-O-(N… · 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 W9BNU9
Elsewhere: RCSB PDB 6HI0 · PDBe 6HI0 · UniProt W9BNU9

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