MolNFT v1 · #169527 · protein
Structure of serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A/V139Q
6XEX: “Structure of serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A/V139Q”. X-ray diffraction, 2 ligands (NAD, NA), 8 pockets (best druggability 0.72). MolNFT v1 #169527 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6XEX
- Type
- protein
- Length
- 504 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, NA
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-butanediol dehydrogenase (EC 1.-.-.-) | protein | 251 | 48% helix, 16% strand | H9XP47 |
| B | 2,3-butanediol dehydrogenase (EC 1.-.-.-) | protein | 253 | 47% helix, 15% strand | H9XP47 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.72 | 0.81 | 53 | NAD, EDO |
| 2 | 392 | 0.59 | 0.76 | 41 | empty |
| 3 | 178 | 0.51 | 0.78 | 23 | empty |
| 4 | 54 | 0.47 | 0.85 | 14 | empty |
| 5 | 120 | 0.41 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1471 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6XEX · Structure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A/V139Q · 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 6XEX · PDBe 6XEX · UniProt H9XP47
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