Research workbench
Adenosylcobinamide KINASE/ADENOSYLCOBINAMIDE phosphate guanylyltransferase (cobu) from salmonella typhimurium
Analyse Adenosylcobinamide KINASE/ADENOSYLCOBINAMIDE phosphate guanylyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CBU
- Type
- protein
- Length
- 539 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylcobinamide KINASE/ADENOSYLCOBINAMIDE phosphate guanylyltransferase
- UniProt
- Q05599
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylcobinamide KINASE/ADENOSYLCOBINAMIDE phosphate guanylyltransferase | protein | 180 | 46% helix, 21% strand | Q05599 |
| C | Adenosylcobinamide KINASE/ADENOSYLCOBINAMIDE phosphate guanylyltransferase | protein | 179 | 43% helix, 21% strand | Q05599 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.72 | 0.76 | 88 | SO4 |
| 2 | 409 | 0.61 | 0.76 | 42 | SO4 |
| 3 | 67 | 0.37 | 0.78 | 12 | empty |
| 4 | 61 | 0.37 | 0.79 | 13 | empty |
| 5 | 59 | 0.35 | 0.78 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 802 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 794 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1CBU · Adenosylcobinamide KINASE/ADENOSYLCOBINAMIDE phosphate guanylyltransferase (cobu) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05599 · AlphaFold monomer V2.0 prediction for bifunctional adenosylcobalamin biosynthesis protein… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q05599
- Elsewhere: RCSB PDB 1CBU · PDBe 1CBU · UniProt Q05599
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