MolNFT v1 · #48031 · protein
The crystal structure of FAD and thdp dependent cyclohexane-1,2-dione hydrolase (cdh) from azoarcus sp. strain 22LIN
2PGO: “The crystal structure of FAD and thdp dependent cyclohexane-1,2-dione hydrolase (cdh) from azoarcus sp.…”. X-ray diffraction, 5 ligands (FAD, TPP, MG), 14 pockets (best druggability 0.87). MolNFT v1 #48031 on GenesisL1: 3D…
- PDB
- 2PGO
- 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, MG, CL, PO4
- Pockets
- 14 · best druggability 0.87
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
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.87 | 0.93 | 92 | CL, MG, FAD, TPP |
| 2 | 716 | 0.86 | 0.90 | 108 | FAD, TPP, MPD, CL |
| 3 | 72 | 0.61 | 0.90 | 20 | empty |
| 4 | 83 | 0.49 | 0.83 | 25 | empty |
| 5 | 81 | 0.42 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 5131 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 2PGO · The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh)… · 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 2PGO · PDBe 2PGO
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