Research workbench
Crystal structure of B. licheniformis cdps yvmc-blic in complex with ches
Analyse Crystal structure of B. licheniformis cdps yvmc-blic in complex with ches in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OQI
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein yvmc
- UniProt
- Q65EX3
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative uncharacterized protein yvmc | protein | 222 | 56% helix, 14% strand | Q65EX3 |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 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 | 663 | 0.78 | 0.83 | 78 | NHE, GOL |
| 2 | 264 | 0.75 | 0.88 | 38 | NHE |
Interfaces
1 interface between chains.
- A–B · 483 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 3OQI · Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex with CHES · the same entry in another collection · chain A against A, TM-score 1.00
- Q65EX3 · AlphaFold monomer V2.0 prediction for CYCLO(L-leucyl-L-leucyl) synthase (Q65EX3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q65EX3
- Elsewhere: RCSB PDB 3OQI · PDBe 3OQI · UniProt Q65EX3
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