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Crystal structure of sdoa from pseudomonas putida in complex with glutathione

Analyse Crystal structure of sdoa from pseudomonas putida in complex with glutathione in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YSL
Type: protein
Length: 588 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase domain protein
UniProt: A5VWI3
Ligands: GSH, FE
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase domain protein	protein	294	24% helix, 28% strand	A5VWI3

Ligands and binding sites

GSH · Glutathione · ligand · 2 copies · chains A, B
FE · Fe (III) ion · metal · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	73	0.62	0.90	17	empty
2	215	0.55	0.78	38	FE, GSH
3	191	0.51	0.77	27	FE, GSH
4	115	0.50	0.80	28	empty

Interfaces

1 interface between chains.

A–B · 1411 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

4YSL · Crystal structure of SdoA from Pseudomonas putida in complex with glutathione · 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 A5VWI3
Elsewhere: RCSB PDB 4YSL · PDBe 4YSL · UniProt A5VWI3

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