Research workbench
Crystal structure of the csid glutarate hydroxylase in complex with succinate
Analyse Crystal structure of the csid glutarate hydroxylase in complex with succinate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HL9
- Type
- protein
- Length
- 593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein csid
- UniProt
- A0A1X3JCQ2
- Ligands
- FE2
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein csid | protein | 299 | 27% helix, 28% strand | A0A1X3JCQ2 |
| B | Protein csid | protein | 294 | 28% helix, 30% strand | A0A1X3JCQ2 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.76 | 0.85 | 48 | FE2, SIN |
| 2 | 358 | 0.68 | 0.81 | 49 | FE2, SIN |
| 3 | 143 | 0.44 | 0.76 | 26 | empty |
| 4 | 130 | 0.39 | 0.74 | 18 | empty |
| 5 | 86 | 0.35 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 531 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HL9 · Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Succinate · 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 A0A1X3JCQ2
- Elsewhere: RCSB PDB 6HL9 · PDBe 6HL9 · UniProt A0A1X3JCQ2
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