MolNFT v1 · #60827 · protein
Crystal structure of yvgn and cofactor NADPH from bacillus subtilis
3D3F · Yvgn protein: “Crystal structure of yvgn and cofactor NADPH from bacillus subtilis”. X-ray diffraction, 1 ligand (NDP), 3 pockets (best druggability 0.82). MolNFT v1 #60827 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3D3F
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yvgn protein
- UniProt
- O32210
- Ligands
- NDP
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Yvgn protein | protein | 275 | 44% helix, 17% strand | O32210 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.82 | 0.84 | 94 | NDP |
| 2 | 258 | 0.68 | 0.84 | 27 | empty |
| 3 | 91 | 0.50 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 792 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 O32210
- Elsewhere: RCSB PDB 3D3F · PDBe 3D3F · UniProt O32210
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