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Klebsiella pneumoniae seryl-tRNA synthetase in complex with the intermediate analog 5'-O-(N-(L-seryl)-SULFAMOYL)ADENOSINE

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

PDB: 6H9X
Type: protein
Length: 428 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine--tRNA ligase
EC: 6.1.1.11
UniProt: W9BNU9
Ligands: SSA, CA
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serine--tRNA ligase (EC 6.1.1.11)	protein	428	44% helix, 21% strand	W9BNU9

Ligands and binding sites

SSA · 5'-O-(N-(L-seryl)-sulfamoyl)adenosine · 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

4 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	584	0.72	0.80	46	SSA, EDO, CA
2	129	0.53	0.81	20	empty
3	66	0.42	0.81	12	EDO
4	79	0.38	0.77	18	empty

Compared structures

6H9X · Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with the Intermediate Analog… · 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 6H9X · PDBe 6H9X · UniProt W9BNU9

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