MolNFT v1 · #61084 · protein
Crystal structure of a putative NADPH-dependent oxidoreductase (DHAF_2064) from desulfitobacterium hafniense dcb-2 at 1.70 a resolution
3DB2: “Crystal structure of a putative NADPH-dependent oxidoreductase (DHAF_2064) from desulfitobacterium hafniense…”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #61084 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DB2
- Type
- protein
- Length
- 1,036 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NADPH-dependent oxidoreductase
- UniProt
- Q18XG3
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative NADPH-dependent oxidoreductase | protein | 347 | 39% helix, 26% strand | Q18XG3 |
| B | Putative NADPH-dependent oxidoreductase | protein | 343 | 40% helix, 26% strand | Q18XG3 |
| C | Putative NADPH-dependent oxidoreductase | protein | 346 | 40% helix, 27% strand | Q18XG3 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.69 | 0.78 | 74 | empty |
| 2 | 500 | 0.63 | 0.75 | 64 | empty |
| 3 | 349 | 0.60 | 0.77 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1998 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 83 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3DB2 · Crystal structure of a putative nadph-dependent oxidoreductase (dhaf_2064) 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 Q18XG3
- Elsewhere: RCSB PDB 3DB2 · PDBe 3DB2 · UniProt Q18XG3
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