Research workbench
The crystal structure of a short-chain DEHYDROGENASES/REDUCTASE (wide type) from veillonella parvula dsm 2008 in complex with NADP
Analyse The crystal structure of a short-chain DEHYDROGENASES/REDUCTASE (wide type)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HNH
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent EPIMERASE/DEHYDRATASE
- UniProt
- D1BQI7
- Ligands
- NAP, TEA, CL
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent EPIMERASE/DEHYDRATASE | protein | 219 | 37% helix, 21% strand | D1BQI7 |
| B | NAD-dependent EPIMERASE/DEHYDRATASE | protein | 217 | 37% helix, 23% strand | D1BQI7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- TEA · Triethylammonium ion · ligand · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
- FMT · Formic acid · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.68 | 0.86 | 43 | FMT, CL |
| 2 | 285 | 0.59 | 0.78 | 43 | NAP, GOL |
| 3 | 220 | 0.56 | 0.79 | 35 | NAP |
| 4 | 96 | 0.38 | 0.76 | 18 | empty |
| 5 | 67 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4HNH · The crystal structure of a short-chain dehydrogenases/reductase (wide type) from… · 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 D1BQI7
- Elsewhere: RCSB PDB 4HNH · PDBe 4HNH · UniProt D1BQI7
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