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Crystal structure of dihydropteroate synthase (folp-SMZ_B27) from soil uncultured bacterium in complex with 6-hydroxymethyl-7,8- dihydropterin pyrophosphate

Analyse Crystal structure of dihydropteroate synthase (folp-SMZ_B27) from soil… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8D5G
Type: protein
Length: 545 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Folp-SMZ_B27
Ligands: HH2, CL
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Folp-SMZ_B27	protein	273	46% helix, 14% strand	—
B	Folp-SMZ_B27	protein	272	45% helix, 14% strand	—

Ligands and binding sites

HH2 · 6-hydroxymethylpterin-diphosphate · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 4 copies · chains A

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

Pockets

3 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	1180	0.82	0.83	105	HH2, CL
2	68	0.41	0.80	15	empty
3	51	0.27	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 785 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

8D5G · Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from soil uncultured… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8D5G · PDBe 8D5G

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