Research workbench
Crystal structure of Csm6 H381A in complex with cA4 by cocrystallization of cA4 and Csm6
Analyse Crystal structure of Csm6 H381A in complex with cA4 by cocrystallization of cA4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O6Z
- Type
- protein
- Length
- 861 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Thermococcus onnurineus (strain NA1)
- Molecule
- Csm6
- UniProt
- B6YWC3
- Ligands
- LQJ
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Csm6 | protein | 431 | 47% helix, 20% strand | B6YWC3 |
| B | Csm6 | protein | 430 | 47% helix, 21% strand | B6YWC3 |
Ligands and binding sites
- LQJ · 3'-O-[(R)-{[(2s,3as,4s,6s,6as)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy) phosphoryl]adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.84 | 0.85 | 80 | empty |
| 2 | 1126 | 0.77 | 0.79 | 67 | LQJ |
| 3 | 391 | 0.61 | 0.77 | 42 | empty |
| 4 | 137 | 0.51 | 0.79 | 28 | empty |
| 5 | 127 | 0.50 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2248 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6O6Z · Crystal structure of CSM6 H381A in complex with CA4 by cocrystallization of CA4 and CSM6 · 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 B6YWC3
- Elsewhere: RCSB PDB 6O6Z · PDBe 6O6Z · UniProt B6YWC3
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