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Crystal structure of helicobacter pylori uree in the apo form

Analyse Crystal structure of helicobacter pylori uree in the apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TJA
Type: protein
Length: 597 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urease accessory protein uree
UniProt: Q09064
Ligands: SO4, CL
Pockets: 4 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Urease accessory protein uree	protein	149	23% helix, 36% strand	Q09064
B, D	Urease accessory protein uree	protein	150	23% helix, 37% strand	Q09064
C	Urease accessory protein uree	protein	148	21% helix, 36% strand	Q09064

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · chains A, C

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	274	0.49	0.73	37	empty
2	128	0.42	0.75	21	empty
3	139	0.39	0.74	22	empty
4	93	0.39	0.76	13	empty

Interfaces

3 interfaces between chains.

A–B · 1158 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1135 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1018 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3TJA · Crystal structure of Helicobacter pylori UreE in the apo form · the same entry in another collection · chain A against A, TM-score 1.00
Q09064 · AlphaFold monomer V2.0 prediction for urease accessory protein uree (Q09064) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q09064
Elsewhere: RCSB PDB 3TJA · PDBe 3TJA · UniProt Q09064

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