Research workbench
Crystal structure of bacillus subtilis yvqk, a putative ATP- binding cobalamin adenosyltransferase, the north east structural genomics target SR128
Analyse Crystal structure of bacillus subtilis yvqk, a putative ATP- binding cobalamin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RTY
- Type
- protein
- Length
- 483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yvqk protein
- UniProt
- O34899
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yvqk protein | protein | 158 | 72% helix, 1% strand | O34899 |
| B | Yvqk protein | protein | 163 | 71% helix, 2% strand | O34899 |
| C | Yvqk protein | protein | 162 | 70% helix, 2% strand | O34899 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.66 | 0.89 | 18 | empty |
| 2 | 393 | 0.58 | 0.75 | 47 | PO4 |
| 3 | 143 | 0.49 | 0.78 | 24 | empty |
| 4 | 122 | 0.48 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1269 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 999 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 981 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 1RTY · Crystal Structure of Bacillus subtilis YvqK, a putative ATP-binding Cobalamin… · the same entry in another collection · chain A against A, TM-score 1.00
- O34899 · AlphaFold monomer V2.0 prediction for corrinoid adenosyltransferase (O34899) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O34899
- Elsewhere: RCSB PDB 1RTY · PDBe 1RTY · UniProt O34899
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