MolNFT v1 · #177067 · protein

Crystal structure of diguanylate cyclase siad in complex with its activator siac from pseudomonas aeruginosa

7E6G · Putative ggdef domain protein: “Crystal structure of diguanylate cyclase siad in complex with its activator siac from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (G2P, MG), 10 pockets (best druggability 0.70). MolNFT v1…

PDB: 7E6G
Type: protein
Length: 1,016 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ggdef domain protein; DUF1987 domain-containing protein
UniProt: A0A069QEY1, A0A072ZHB4
Ligands: G2P, MG
Pockets: 10 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 51% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative ggdef domain protein	protein	264	63% helix, 13% strand	A0A069QEY1
B	Putative ggdef domain protein	protein	260	64% helix, 14% strand	A0A069QEY1
C	DUF1987 domain-containing protein	protein	124	37% helix, 31% strand	A0A072ZHB4
D	DUF1987 domain-containing protein	protein	125	37% helix, 30% strand	A0A072ZHB4
E	DUF1987 domain-containing protein	protein	121	40% helix, 31% strand	A0A072ZHB4
F	DUF1987 domain-containing protein	protein	122	39% helix, 31% strand	A0A072ZHB4

Ligands and binding sites

G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	581	0.70	0.79	51	empty
2	701	0.68	0.76	79	MG, G2P
3	303	0.58	0.77	40	empty
4	311	0.58	0.77	35	empty
5	258	0.52	0.75	33	empty

Interfaces

11 interfaces between chains.

A–B · 2858 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 872 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 871 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 814 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 761 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7E6G · Crystal structure of diguanylate cyclase SiaD in complex with its activator SiaC from… · 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 A0A069QEY1
Every structure of UniProt A0A072ZHB4
Elsewhere: RCSB PDB 7E6G · PDBe 7E6G · UniProt A0A069QEY1 · UniProt A0A072ZHB4

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