Research workbench
Crystal structure of the csid glutarate hydroxylase in complex with glutarate
Analyse Crystal structure of the csid glutarate hydroxylase in complex with glutarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HL8
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein csid
- UniProt
- P76621
- Ligands
- GUA, FE2
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein csid | protein | 291 | 29% helix, 30% strand | P76621 |
| B | Protein csid | protein | 292 | 29% helix, 29% strand | P76621 |
Ligands and binding sites
- GUA · Glutaric acid · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.67 | 0.80 | 44 | FE2, GUA |
| 2 | 373 | 0.66 | 0.80 | 38 | FE2, GUA |
| 3 | 293 | 0.54 | 0.75 | 41 | empty |
| 4 | 157 | 0.40 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 688 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6HL8 · Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Glutarate · 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 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 P76621
- Elsewhere: RCSB PDB 6HL8 · PDBe 6HL8 · UniProt P76621
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