MolNFT v1 · #150760 · protein
Staphylopine dehydrogenase in complex with staphylopine and NADP+
6H3F: “Staphylopine dehydrogenase in complex with staphylopine and NADP+”. X-ray diffraction, 2 ligands (NAP, 8UX), 2 pockets (best druggability 0.81). MolNFT v1 #150760 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6H3F
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Staphylopine dehydrogenase
- UniProt
- A0A0H3JNH9
- Ligands
- NAP, 8UX
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylopine dehydrogenase | protein | 428 | 46% helix, 15% strand | A0A0H3JNH9 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- 8UX · (2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid · ligand · chains A
- GOL · Glycerol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.81 | 0.94 | 26 | PG4 |
| 2 | 969 | 0.77 | 0.79 | 90 | NAP, 8UX |
Compared structures
- 6H3F · Staphylopine dehydrogenase in complex with staphylopine and NADP+ · 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 A0A0H3JNH9
- Elsewhere: RCSB PDB 6H3F · PDBe 6H3F · UniProt A0A0H3JNH9
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