Research workbench
The crystal structure of FAD and thdp-dependent cyclohexane-1,2-dione hydrolase in complex with cyclohexane-1,2-dione
Analyse The crystal structure of FAD and thdp-dependent cyclohexane-1,2-dione hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PGN
- Type
- protein
- Length
- 1,174 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclohexane-1,2-dione hydrolase (cdh)
- Ligands
- FAD, TPP, CXO, MG
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclohexane-1,2-dione hydrolase (cdh) | protein | 587 | 40% helix, 16% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- CXO · Cyclohexane-1,2-dione · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.88 | 0.94 | 97 | MG, FAD, TPP, CXO |
| 2 | 568 | 0.87 | 0.93 | 95 | CXO, MG, FAD, TPP |
| 3 | 62 | 0.59 | 0.90 | 19 | empty |
| 4 | 102 | 0.54 | 0.84 | 26 | empty |
| 5 | 137 | 0.41 | 0.75 | 25 | P6G |
Interfaces
1 interface between chains.
- A–B · 5145 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 2PGN · The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in… · 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
- Elsewhere: RCSB PDB 2PGN · PDBe 2PGN
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