MolNFT v1 · #153576 · protein
Complex structure of an imine reductase at 2.05 ångström resolution
6JIT · 6-phosphogluconate dehydrogenase NAD-binding protein: “Complex structure of an imine reductase at 2.05 ångström resolution”. X-ray diffraction, 3 ligands (LW7, NAP, CL), 6 pockets (best druggability 0.80). MolNFT v1 #153576 on…
- PDB
- 6JIT
- Type
- protein
- Length
- 863 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase NAD-binding protein
- UniProt
- D3Q3R0
- Ligands
- LW7, NAP, CL
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase NAD-binding protein | protein | 284 | 60% helix, 14% strand | D3Q3R0 |
| B | 6-phosphogluconate dehydrogenase NAD-binding protein | protein | 287 | 58% helix, 13% strand | D3Q3R0 |
| C | 6-phosphogluconate dehydrogenase NAD-binding protein | protein | 292 | 57% helix, 13% strand | D3Q3R0 |
Ligands and binding sites
- LW7 · 1-(2-phenylethyl)-3,4-dihydroisoquinoline · ligand · chains B, C
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, C
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.80 | 0.86 | 64 | LW7, NAP |
| 2 | 577 | 0.68 | 0.77 | 50 | empty |
| 3 | 501 | 0.61 | 0.74 | 35 | empty |
| 4 | 332 | 0.60 | 0.78 | 56 | empty |
| 5 | 100 | 0.32 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4213 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 729 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 246 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6JIT · Complex structure of an imine reductase at 2.05 Angstrom resolution · 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 D3Q3R0
- Elsewhere: RCSB PDB 6JIT · PDBe 6JIT · UniProt D3Q3R0
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