MolNFT v1 · #62805 · protein
Crystal structure of the yubc protein from bacillus subtilis. northeast structural genomics consortium target SR112.
3EQE · Putative cystein dioxygenase: “Crystal structure of the yubc protein from bacillus subtilis. northeast structural genomics consortium target…”. X-ray diffraction, 1 ligand (FE), 3 pockets (best druggability 0.38). MolNFT v1 #62805…
- 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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