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Crystal structure of the pebp-like protein of unknown function HP0218 from helicobacter pylori

Analyse Crystal structure of the pebp-like protein of unknown function HP0218 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EVV
Type: protein
Length: 724 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein HP0218
UniProt: O25006
Ligands: SO4
Pockets: 8 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Hypothetical protein HP0218	protein	181	18% helix, 29% strand	O25006
B	Hypothetical protein HP0218	protein	182	18% helix, 28% strand	O25006
D	Hypothetical protein HP0218	protein	180	19% helix, 28% strand	O25006

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	339	0.62	0.78	39	GOL
2	404	0.59	0.75	55	GOL
3	259	0.58	0.78	43	empty
4	241	0.55	0.77	35	empty
5	111	0.47	0.79	21	GOL

Interfaces

6 interfaces between chains.

A–B · 1705 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1701 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 336 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 171 Å² buried · 1 hydrogen bond · protein-protein
A–C · 148 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 modified (engineered).

Compared structures

2EVV · Crystal Structure of the PEBP-like Protein of Unknown Function HP0218 from Helicobacter… · 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 O25006
Elsewhere: RCSB PDB 2EVV · PDBe 2EVV · UniProt O25006

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