Research workbench
Crystal structure of H. pylori htra with PDZ2 deletion
Analyse Crystal structure of H. pylori htra with PDZ2 deletion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y28
- Type
- protein
- Length
- 752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic serine endoprotease degp-like; Unk-unk-unk-unk
- EC
- 3.4.21.107
- UniProt
- G2J5T2
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic serine endoprotease degp-like (EC 3.4.21.107) | protein | 268 | 12% helix, 31% strand | G2J5T2 |
| B | Periplasmic serine endoprotease degp-like (EC 3.4.21.107) | protein | 202 | 14% helix, 37% strand | G2J5T2 |
| C | Periplasmic serine endoprotease degp-like (EC 3.4.21.107) | protein | 278 | 14% helix, 34% strand | G2J5T2 |
| G | Unk-unk-unk-unk | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.62 | 0.79 | 44 | empty |
| 2 | 180 | 0.52 | 0.79 | 29 | empty |
| 3 | 71 | 0.31 | 0.74 | 21 | empty |
| 4 | 51 | 0.30 | 0.76 | 10 | EDO |
| 5 | 62 | 0.28 | 0.74 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1824 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1780 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1619 Ų buried · 30 hydrogen bonds · protein-protein
- A–G · 243 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5Y28 · Crystal structure of H. pylori HtrA with PDZ2 deletion · 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 G2J5T2
- Elsewhere: RCSB PDB 5Y28 · PDBe 5Y28 · UniProt G2J5T2
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