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Pdua K26A, crystal form 2

Analyse Pdua K26A, crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PPD
Type: protein
Length: 610 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 0.71

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	92	33% helix, 36% strand	P0A1C7
B	Propanediol utilization protein pdua	protein	91	33% helix, 38% strand	P0A1C7
C	Propanediol utilization protein pdua	protein	82	37% helix, 38% strand	P0A1C7
D	Propanediol utilization protein pdua	protein	87	34% helix, 37% strand	P0A1C7
E	Propanediol utilization protein pdua	protein	84	36% helix, 38% strand	P0A1C7
F	Propanediol utilization protein pdua	protein	88	38% helix, 33% strand	P0A1C7
G	Propanediol utilization protein pdua	protein	86	36% helix, 37% strand	P0A1C7

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, D, B, C, G
GOL · Glycerol · additive · 2 copies · chains A, B, E, F, G

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

Pockets

5 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	689	0.71	0.78	54	SO4
2	111	0.49	0.81	25	empty
3	133	0.46	0.77	25	empty
4	61	0.35	0.78	12	empty
5	62	0.34	0.77	17	empty

Interfaces

10 interfaces between chains.

F–G · 837 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 810 Å² buried · 12 hydrogen bonds · protein-protein
E–G · 797 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 779 Å² buried · 8 hydrogen bonds · protein-protein
A–G · 456 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4PPD · PduA K26A, crystal form 2 · 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 0.97

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 4PPD · PDBe 4PPD · UniProt P0A1C7

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