Research workbench
Crystal structure of ycei (HP1286) from helicobacter pylori
Analyse Crystal structure of ycei (HP1286) 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
- 3HPE
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical secreted protein
- UniProt
- Q1CRX8
- Ligands
- ERU
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Conserved hypothetical secreted protein | protein | 164 | 9% helix, 59% strand | Q1CRX8 |
Ligands and binding sites
- ERU · (13Z)-docos-13-enamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.83 | 0.90 | 62 | ERU |
| 2 | 449 | 0.82 | 0.88 | 55 | ERU |
Interfaces
1 interface between chains.
- A–B · 1408 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3HPE · Crystal structure of yceI (HP1286) from Helicobacter pylori · 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 Q1CRX8
- Elsewhere: RCSB PDB 3HPE · PDBe 3HPE · UniProt Q1CRX8
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