MolNFT v1 · #88781 · protein
Crystal structure of recombinant wildtype cdh
4D5E · Cyclohexane-1,2-dione hydrolase: “Crystal structure of recombinant wildtype cdh”. X-ray diffraction, 5 ligands (FAD, TPP, 1PG), 11 pockets (best druggability 0.87). MolNFT v1 #88781 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4D5E
- Type
- protein
- Length
- 1,173 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclohexane-1,2-dione hydrolase
- EC
- 3.7.1.11
- UniProt
- P0CH62
- Ligands
- FAD, TPP, 1PG, MG, CL
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclohexane-1,2-dione hydrolase (EC 3.7.1.11) | protein | 586 | 41% helix, 16% strand | P0CH62 |
| B | Cyclohexane-1,2-dione hydrolase (EC 3.7.1.11) | protein | 587 | 40% helix, 16% strand | P0CH62 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 9 copies · chains A, B
- 2PE · Nonaethylene glycol · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.87 | 0.91 | 110 | FAD, TPP, MG, CL |
| 2 | 702 | 0.87 | 0.90 | 102 | CL, FAD, TPP |
| 3 | 164 | 0.43 | 0.75 | 25 | PG4 |
| 4 | 68 | 0.42 | 0.81 | 24 | empty |
| 5 | 155 | 0.42 | 0.74 | 22 | PG4 |
Interfaces
1 interface between chains.
- A–B · 5160 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
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 P0CH62
- Elsewhere: RCSB PDB 4D5E · PDBe 4D5E · UniProt P0CH62
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