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

Analyse Crystal structure of diguanylate cyclase siad in complex with its activator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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

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Every structure of UniProt A0A069QEY1
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Elsewhere: RCSB PDB 7E6G · PDBe 7E6G · UniProt A0A069QEY1 · UniProt A0A072ZHB4

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