Research workbench
Crystal structure of CSD1-CSD2 dimer II
Analyse Crystal structure of CSD1-CSD2 dimer II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J1M
- Type
- protein
- Length
- 678 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxr-activated gene (tage)
- UniProt
- O26068, O26069
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxr-activated gene (tage) | protein | 166 | 26% helix, 31% strand | O26068 |
| B | Toxr-activated gene (tage) | protein | 176 | 20% helix, 32% strand | O26069 |
| C | Toxr-activated gene (tage) | protein | 159 | 22% helix, 31% strand | O26068 |
| D | Toxr-activated gene (tage) | protein | 177 | 23% helix, 31% 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.57 | 0.78 | 34 | empty |
| 2 | 126 | 0.42 | 0.76 | 23 | empty |
| 3 | 131 | 0.39 | 0.74 | 20 | empty |
| 4 | 84 | 0.39 | 0.77 | 20 | empty |
| 5 | 59 | 0.37 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1490 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1443 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 353 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 326 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 314 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5J1M · Crystal structure of Csd1-Csd2 dimer II · 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 5J1M · PDBe 5J1M · UniProt O26068 · UniProt O26069
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