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Crystal structure of Glyoxalase/bleomycin resistance protein/dioxygenase from Conexibacter woesei DSM 14684
Analyse Crystal structure of Glyoxalase/bleomycin resistance protein/dioxygenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GYM
- Type
- protein
- Length
- 283 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.56
- Source
- Conexibacter woesei
- Molecule
- Glyoxalase/bleomycin resistance protein/dioxygenase
- UniProt
- D3F7P7
- Ligands
- K, NA
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.56 · 2 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyoxalase/bleomycin resistance protein/dioxygenase | protein | 138 | 24% helix, 36% strand | D3F7P7 |
| B | Glyoxalase/bleomycin resistance protein/dioxygenase | protein | 145 | 31% helix, 37% strand | D3F7P7 |
Ligands and binding sites
- K · Potassium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 404 | 0.72 | 0.83 | 53 | TRS |
| 2 | 424 | 0.66 | 0.78 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 2842 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4GYM · Crystal structure of GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE from… · the same entry in another collection · chain A against A, TM-score 1.00
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 D3F7P7
- Elsewhere: RCSB PDB 4GYM · PDBe 4GYM · UniProt D3F7P7
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