MolNFT v1 · #169526 · protein
Structure of serratia marcescens 2,3-butanediol dehydrogenase
6XEW: “Structure of serratia marcescens 2,3-butanediol dehydrogenase”. X-ray diffraction, 4 ligands (NAD, HBR, HBS), 7 pockets (best druggability 0.72). MolNFT v1 #169526 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XEW
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-butanediol dehydrogenase
- EC
- 1.-.-.-
- UniProt
- H9XP47
- Ligands
- NAD, HBR, HBS, ADP
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2,3-butanediol dehydrogenase (EC 1.-.-.-) | protein | 251 | 48% helix, 16% strand | H9XP47 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A
- HBR · R,3-hydroxybutan-2-one · ligand · chains A
- HBS · S,3-hydroxybutan-2-one · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.72 | 0.81 | 55 | NAD, HBR, HBS |
| 2 | 518 | 0.65 | 0.77 | 50 | ADP |
| 3 | 170 | 0.51 | 0.78 | 23 | empty |
| 4 | 97 | 0.39 | 0.77 | 21 | empty |
| 5 | 117 | 0.39 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1394 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6XEW · Structure of Serratia marcescens 2,3-butanediol dehydrogenase · 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 H9XP47
- Elsewhere: RCSB PDB 6XEW · PDBe 6XEW · UniProt H9XP47
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