Research workbench
Structure of helicobacter pylori CSD3 from the orthorhombic crystal
Analyse Structure of helicobacter pylori CSD3 from the orthorhombic crystal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RNY
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical secreted protein
- UniProt
- O25247
- Ligands
- ZN, SO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Conserved hypothetical secreted protein | protein | 359 | 19% helix, 42% strand | O25247 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.81 | 0.84 | 84 | SO4 |
| 2 | 240 | 0.76 | 0.90 | 39 | GOL |
| 3 | 330 | 0.76 | 0.87 | 55 | GOL |
| 4 | 183 | 0.56 | 0.80 | 27 | SO4 |
| 5 | 138 | 0.54 | 0.82 | 23 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1216 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4RNY · Structure of Helicobacter pylori Csd3 from the orthorhombic crystal · 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 O25247
- Elsewhere: RCSB PDB 4RNY · PDBe 4RNY · UniProt O25247
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