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Pgpg-specific phosphodiesterase - pggh from vibrio cholrae

Analyse Pgpg-specific phosphodiesterase - pggh from vibrio cholrae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D62
Type: protein
Length: 587 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pggh
UniProt: Q9KLZ6
Ligands: MN, SO4
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pggh	protein	294	43% helix, 18% strand	Q9KLZ6
B	Pggh	protein	293	43% helix, 18% strand	Q9KLZ6

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

2 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	969	0.86	0.88	96	SO4
2	991	0.75	0.78	85	MN

Interfaces

1 interface between chains.

A–B · 1722 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7D62 · pGpG-specific phosphodiesterase - PggH from Vibrio cholrae · 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 Q9KLZ6
Elsewhere: RCSB PDB 7D62 · PDBe 7D62 · UniProt Q9KLZ6

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