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H.PYLORI beta clamp in complex with diflunisal

Analyse H.PYLORI beta clamp in complex with diflunisal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5G48
Type: protein
Length: 744 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase III subunit beta
UniProt: O25242
Ligands: 1FL
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase III subunit beta	protein	370	21% helix, 40% strand	O25242
B	DNA polymerase III subunit beta	protein	374	21% helix, 40% strand	O25242

Ligands and binding sites

1FL · 5-(2,4-difluorophenyl)-2-hydroxy-benzoic acid · ligand · 2 copies · chains A, B

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

Pockets

6 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	781	0.69	0.76	78	empty
2	175	0.50	0.78	25	empty
3	139	0.43	0.76	28	empty
4	81	0.34	0.75	16	empty
5	52	0.33	0.78	14	1FL

Interfaces

1 interface between chains.

A–B · 662 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5G48 · H.pylori Beta clamp in complex with Diflunisal · the same entry in another collection · chain A against A, TM-score 1.00
O25242 · AlphaFold monomer V2.0 prediction for beta sliding clamp (O25242) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O25242
Elsewhere: RCSB PDB 5G48 · PDBe 5G48 · UniProt O25242

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