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Crystal structure of an exopolyphosphatase-related protein from bacteroides fragilis. northeast structural genomics target BFR192

Analyse Crystal structure of an exopolyphosphatase-related protein from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PY9
Type: protein
Length: 340 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative exopolyphosphatase-related protein
UniProt: Q64PD9
Ligands: NA, PO4
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative exopolyphosphatase-related protein	protein	340	46% helix, 17% strand	Q64PD9

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A
PO4 · Phosphate ion · ion · 4 copies · 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	1030	0.71	0.75	76	PO4, NA
2	66	0.43	0.81	14	NA

Modifications

Observed in the structure: 11 modified (engineered).

Compared structures

4PY9 · Crystal structure of an exopolyphosphatase-related protein from Bacteroides Fragilis.… · 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 Q64PD9
Elsewhere: RCSB PDB 4PY9 · PDBe 4PY9 · UniProt Q64PD9

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