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Structure of pseudomonas fluorescence lapd eal domain complexed with C-di-gmp, P6522

Analyse Structure of pseudomonas fluorescence lapd eal domain complexed with C-di-gmp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PJU
Type: protein
Length: 249 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic dimeric gmp binding protein
UniProt: Q3KK31
Ligands: C2E
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclic dimeric gmp binding protein	protein	249	49% helix, 20% strand	Q3KK31

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 · chains A

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

Pockets

2 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	285	0.64	0.81	37	C2E
2	133	0.43	0.76	21	empty

Compared structures

3PJU · Structure of Pseudomonas fluorescence LapD EAL domain complexed with c-di-GMP, P6522 · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q3KK31
Elsewhere: RCSB PDB 3PJU · PDBe 3PJU · UniProt Q3KK31

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