Research workbench

Crystal structure of protein LPP20 (HP1456) from helicobacter pylori

Analyse Crystal structure of protein LPP20 (HP1456) from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OK8
Type: protein
Length: 457 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LPP20 lipoprotein
UniProt: P0A0V1
Ligands: CA
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	LPP20 lipoprotein	protein	114	55% helix, 22% strand	P0A0V1
B	LPP20 lipoprotein	protein	115	55% helix, 22% strand	P0A0V1

Ligands and binding sites

CA · Calcium ion · metal · chains B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, C

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

Pockets

6 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	823	0.74	0.79	81	EPE, CA
2	59	0.36	0.79	14	empty
3	77	0.35	0.76	18	empty
4	88	0.34	0.74	14	empty
5	56	0.28	0.73	10	empty

Interfaces

4 interfaces between chains.

C–D · 527 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 312 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 200 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 58 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5OK8 · Crystal structure of protein Lpp20 (HP1456) from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
P0A0V1 · AlphaFold monomer V2.0 prediction for LPP20 lipoprotein (P0A0V1) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P0A0V1
Elsewhere: RCSB PDB 5OK8 · PDBe 5OK8 · UniProt P0A0V1

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