Research workbench
Crystal Structure of the CsiD Glutarate Hydroxylase in complex with N-Oxalylglycine
Analyse Crystal Structure of the CsiD Glutarate Hydroxylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GPN
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Escherichia coli (strain K12)
- Molecule
- Glutarate 2-hydroxylase
- EC
- 1.14.11.64
- UniProt
- P76621
- Ligands
- OGA, FE2
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutarate 2-hydroxylase (EC 1.14.11.64) | protein | 289 | 29% helix, 30% strand | P76621 |
| B | Glutarate 2-hydroxylase (EC 1.14.11.64) | protein | 292 | 29% helix, 30% strand | P76621 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.62 | 0.79 | 39 | FE2, OGA |
| 2 | 203 | 0.55 | 0.78 | 26 | FE2 |
| 3 | 181 | 0.45 | 0.74 | 31 | empty |
| 4 | 146 | 0.41 | 0.74 | 19 | empty |
| 5 | 64 | 0.37 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 574 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GPN · Crystal structure of the csid glutarate hydroxylase in complex with N- oxalylglycine · the same entry in another collection · chain A against A, TM-score 1.00
- P76621 · AlphaFold monomer V2.0 prediction for glutarate 2-hydroxylase (P76621) · a predicted model of the same protein · chain B 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 P76621
- Elsewhere: RCSB PDB 6GPN · PDBe 6GPN · UniProt P76621
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