Research workbench
Crystal structure of the yubc protein from bacillus subtilis. northeast structural genomics consortium target SR112.
Analyse Crystal structure of the yubc protein from bacillus subtilis. northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EQE
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cystein dioxygenase
- EC
- 1.13.11.-
- UniProt
- O32085
- Ligands
- FE
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative cystein dioxygenase (EC 1.13.11.-) | protein | 156 | 14% helix, 40% strand | O32085 |
| B | Putative cystein dioxygenase (EC 1.13.11.-) | protein | 154 | 13% helix, 38% strand | O32085 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.38 | 0.76 | 18 | empty |
| 2 | 90 | 0.38 | 0.76 | 15 | empty |
| 3 | 85 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 482 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3EQE · Crystal structure of the YubC protein from Bacillus subtilis. Northeast Structural… · the same entry in another collection · chain A against A, TM-score 1.00
- O32085 · AlphaFold monomer V2.0 prediction for cysteine dioxygenase (O32085) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O32085
- Elsewhere: RCSB PDB 3EQE · PDBe 3EQE · UniProt O32085
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