Research workbench

Ybgc thioesterase (HP0496) from helicobacter pylori

Analyse Ybgc thioesterase (HP0496) 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: 2PZH
Type: protein
Length: 533 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein HP_0496
UniProt: P94842
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein HP_0496	protein	134	19% helix, 45% strand	P94842
C, D, B	Hypothetical protein HP_0496	protein	133	20% helix, 43% strand	P94842

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.81	0.90	39	empty
2	271	0.81	0.92	38	empty
3	340	0.79	0.89	45	empty
4	250	0.77	0.90	38	empty
5	69	0.69	0.96	30	empty

Interfaces

6 interfaces between chains.

C–B · 1060 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1056 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1006 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1000 Å² buried · 10 hydrogen bonds · protein-protein
D–B · 375 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2PZH · YbgC thioesterase (Hp0496) from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
P94842 · AlphaFold monomer V2.0 prediction for acyl-CoA thioesterase ybgc (P94842) · a predicted model of the same protein · chain C 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 P94842
Elsewhere: RCSB PDB 2PZH · PDBe 2PZH · UniProt P94842

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