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Structure of the ALG44 pilz domain from pseudomonas aeruginosa PAO1 in complex with C-di-gmp

Analyse Structure of the ALG44 pilz domain from pseudomonas aeruginosa PAO1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RT0
Type: protein
Length: 323 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alginate biosynthesis protein ALG44
UniProt: Q9HY69
Ligands: C2E
Pockets: 7 · best druggability 0.38

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alginate biosynthesis protein ALG44	protein	109	16% helix, 46% strand	Q9HY69
B	Alginate biosynthesis protein ALG44	protein	107	18% helix, 48% strand	Q9HY69
C	Alginate biosynthesis protein ALG44	protein	107	15% helix, 50% strand	Q9HY69

Ligands and binding sites

C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 6 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 2 copies · chains C

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

Pockets

7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.38	0.76	20	empty
2	81	0.36	0.76	17	C2E
3	65	0.34	0.77	16	empty
4	71	0.33	0.76	18	C2E
5	65	0.31	0.76	17	C2E

Interfaces

3 interfaces between chains.

B–C · 730 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 225 Å² buried · 1 hydrogen bond · protein-protein
A–B · 51 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (engineered).

Compared structures

4RT0 · Structure of the Alg44 PilZ domain from Pseudomonas aeruginosa PAO1 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Q9HY69 · AlphaFold monomer V2.0 prediction for mannuronan synthase (Q9HY69) · a predicted model of the same protein · chain C against A, TM-score 0.90

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 Q9HY69
Elsewhere: RCSB PDB 4RT0 · PDBe 4RT0 · UniProt Q9HY69

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