MolNFT v1 · #118192 · protein

Crystal structure of the C-di-gmp-bound ggdef domain of P. fluorescens gcbc

5EUH · Putative ggdef domain membrane protein: “Crystal structure of the C-di-gmp-bound ggdef domain of P. fluorescens gcbc”. X-ray diffraction, 2 ligands (C2E, SO4), 6 pockets (best druggability 0.80). MolNFT v1 #118192 on GenesisL1: 3D…

PDB: 5EUH
Type: protein
Length: 612 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ggdef domain membrane protein
UniProt: Q3K751
Ligands: C2E, SO4
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative ggdef domain membrane protein	protein	164	49% helix, 20% strand	Q3K751
C	Putative ggdef domain membrane protein	protein	142	42% helix, 17% strand	Q3K751
D	Putative ggdef domain membrane protein	protein	142	47% helix, 15% strand	Q3K751

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 · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D

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

Pockets

6 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	1065	0.80	0.81	91	SO4
2	383	0.65	0.79	36	empty
3	148	0.43	0.75	20	empty
4	73	0.35	0.76	17	empty
5	51	0.30	0.76	14	empty

Interfaces

5 interfaces between chains.

A–D · 485 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 481 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 461 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 352 Å² buried · 1 hydrogen bond · protein-protein
A–C · 11 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5EUH · Crystal structure of the c-di-GMP-bound GGDEF domain of P. fluorescens GcbC · the same entry in another collection · chain A against A, TM-score 1.00

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 Q3K751
Elsewhere: RCSB PDB 5EUH · PDBe 5EUH · UniProt Q3K751

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