Research workbench
Crystal structure of listeria monocytogenes cbpb protein (LMO1009) in complex with C-di-AMP
Analyse Crystal structure of listeria monocytogenes cbpb protein (LMO1009) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XNV
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cbs domain-containing protein
- UniProt
- A0A1D2IWV8
- Ligands
- 2BA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cbs domain-containing protein | protein | 133 | 42% helix, 26% strand | A0A1D2IWV8 |
| B | Cbs domain-containing protein | protein | 132 | 40% helix, 27% strand | A0A1D2IWV8 |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.71 | 0.78 | 66 | 2BA |
| 2 | 200 | 0.51 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1320 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6XNV · Crystal structure of listeria monocytogenes cbpb protein (LMO1009) in complex with… · 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 A0A1D2IWV8
- Elsewhere: RCSB PDB 6XNV · PDBe 6XNV · UniProt A0A1D2IWV8
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