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Pdua K26A S40GSG mutant, from salmonella enterica serovar typhimurium LT2

Analyse Pdua K26A S40GSG 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: 4RBV
Type: protein
Length: 627 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Propanediol utilization protein pdua
UniProt: P0A1C7
Ligands: SO4
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 7 distinct chains · 35% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Propanediol utilization protein pdua	protein	93	37% helix, 37% strand	P0A1C7
B	Propanediol utilization protein pdua	protein	94	31% helix, 37% strand	P0A1C7
C	Propanediol utilization protein pdua	protein	85	34% helix, 39% strand	P0A1C7
D	Propanediol utilization protein pdua	protein	89	38% helix, 38% strand	P0A1C7
E	Propanediol utilization protein pdua	protein	87	32% helix, 37% strand	P0A1C7
F	Propanediol utilization protein pdua	protein	90	37% helix, 32% strand	P0A1C7
G	Propanediol utilization protein pdua	protein	89	35% helix, 38% strand	P0A1C7

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, G, D

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

Pockets

5 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	872	0.74	0.78	55	SO4
2	160	0.51	0.79	30	empty
3	88	0.43	0.79	23	empty
4	92	0.43	0.79	23	empty
5	53	0.33	0.78	16	empty

Interfaces

11 interfaces between chains.

F–G · 866 Å² buried · 11 hydrogen bonds · protein-protein
E–G · 830 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 807 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 777 Å² buried · 8 hydrogen bonds · protein-protein
D–G · 423 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4RBV · PduA K26A S40GSG mutant, from Salmonella enterica serovar Typhimurium LT2 · the same entry in another collection · chain G against G, TM-score 1.00
P0A1C7 · AlphaFold monomer V2.0 prediction for propanediol utilization protein pdua (P0A1C7) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 4RBV · PDBe 4RBV · UniProt P0A1C7

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