Research workbench
Crystal structure of Csd1-Csd2 dimer I
Analyse Crystal structure of Csd1-Csd2 dimer I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J1L
- Type
- protein
- Length
- 679 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.27
- Source
- Helicobacter pylori; Helicobacter pylori (strain ATCC 700392 / 26695)
- Molecule
- ToxR-activated gene (TagE)
- UniProt
- O26068, O26069
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · resolution 2.27 · 4 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ToxR-activated gene (TagE) | protein | 160 | 27% helix, 31% strand | O26068 |
| B | ToxR-activated gene (TagE) | protein | 182 | 21% helix, 31% strand | O26069 |
| C | ToxR-activated gene (TagE) | protein | 162 | 23% helix, 33% strand | O26068 |
| D | ToxR-activated gene (TagE) | protein | 175 | 21% helix, 30% strand | O26069 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.57 | 0.78 | 30 | empty |
| 2 | 129 | 0.50 | 0.80 | 28 | empty |
| 3 | 96 | 0.49 | 0.82 | 21 | empty |
| 4 | 178 | 0.46 | 0.76 | 30 | empty |
| 5 | 164 | 0.45 | 0.75 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1351 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1316 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 341 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 288 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5J1L · Crystal structure of CSD1-CSD2 dimer I · 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 O26068
- Every structure of UniProt O26069
- Elsewhere: RCSB PDB 5J1L · PDBe 5J1L · UniProt O26068 · UniProt O26069
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