MolNFT v1 · #170798 · protein
Darb fom B. subtilis in complex with AMP
6YJ7 · Cbs domain-containing protein ykul: “Darb fom B. subtilis in complex with AMP”. X-ray diffraction, 2 ligands (AMP, CL), 2 pockets (best druggability 0.69). MolNFT v1 #170798 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6YJ7
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cbs domain-containing protein ykul
- UniProt
- O31698
- Ligands
- AMP, CL
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cbs domain-containing protein ykul | protein | 142 | 46% helix, 27% strand | O31698 |
| B | Cbs domain-containing protein ykul | protein | 134 | 41% helix, 28% strand | O31698 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.69 | 0.76 | 54 | AMP, CL |
| 2 | 66 | 0.36 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1364 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 O31698
- Elsewhere: RCSB PDB 6YJ7 · PDBe 6YJ7 · UniProt O31698
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