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Pdua K26A S40Q mutant, from salmonella enterica serovar typhimurium LT2

Analyse Pdua K26A S40Q mutant, from salmonella enterica serovar typhimurium LT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RBU
Type: protein
Length: 792 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Propanediol utilization protein pdua
UniProt: P0A1C7
Ligands: SO4
Pockets: 6 · best druggability 0.52

Structure

x-ray diffraction · 5 distinct chains · 36% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, H, I	Propanediol utilization protein pdua	protein	87	37% helix, 39% strand	P0A1C7
C	Propanediol utilization protein pdua	protein	88	34% helix, 39% strand	P0A1C7
D	Propanediol utilization protein pdua	protein	89	37% helix, 38% strand	P0A1C7
E, F	Propanediol utilization protein pdua	protein	89	37% helix, 37% strand	P0A1C7
G	Propanediol utilization protein pdua	protein	89	35% helix, 38% strand	P0A1C7

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, D, B, C, E, G, H, I

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

Pockets

6 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	274	0.52	0.75	24	SO4
2	84	0.43	0.80	15	empty
3	69	0.34	0.76	17	empty
4	63	0.33	0.76	16	empty
5	52	0.30	0.76	17	empty

Interfaces

14 interfaces between chains.

D–F · 886 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 882 Å² buried · 15 hydrogen bonds · protein-protein
G–I · 863 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 855 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 839 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4RBU · PduA K26A S40Q mutant, from Salmonella enterica serovar Typhimurium LT2 · the same entry in another collection · chain I against I, TM-score 1.00
P0A1C7 · AlphaFold monomer V2.0 prediction for propanediol utilization protein pdua (P0A1C7) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P0A1C7
Elsewhere: RCSB PDB 4RBU · PDBe 4RBU · UniProt P0A1C7

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