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Crystal structure of the helicobacter pylori ATPase, HP0525, in complex with ADP

Analyse Crystal structure of the helicobacter pylori ATPase, HP0525, in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1G6O
Type: protein
Length: 646 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cag-alpha
Ligands: ADP
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cag-alpha	protein	323	39% helix, 21% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1078	0.82	0.83	98	ADP
2	443	0.72	0.82	53	ADP
3	728	0.71	0.77	58	empty
4	69	0.39	0.79	15	empty
5	60	0.37	0.79	14	empty

Interfaces

1 interface between chains.

A–B · 1906 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

1G6O · Crystal structure of the helicobacter pylori ATPase, HP0525, in complex with ADP · 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
Elsewhere: RCSB PDB 1G6O · PDBe 1G6O

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