Research workbench
Apo structure of an imine reductase at 1.76 ångström resolution
Analyse Apo structure of an imine reductase at 1.76 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JIZ
- Type
- protein
- Length
- 881 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
- LW9, NAP, NA, CL, NH4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 6-phosphogluconate dehydrogenase NAD-binding protein | protein | 293 | 58% helix, 12% strand | D3Q3R0 |
| C | 6-phosphogluconate dehydrogenase NAD-binding protein | protein | 295 | 59% helix, 13% strand | D3Q3R0 |
Ligands and binding sites
- LW9 · 3-ethylheptane · ligand · chains B, C
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains B, C
- NA · Sodium ion · metal · 2 copies · chains A, B, C
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- NH4 · Ammonium ion · ion · chains A
- ACT · Acetate ion · additive · 7 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.78 | 0.87 | 56 | LW9, NAP |
| 2 | 578 | 0.66 | 0.76 | 54 | empty |
| 3 | 340 | 0.59 | 0.77 | 48 | ACT |
| 4 | 381 | 0.57 | 0.74 | 32 | empty |
| 5 | 108 | 0.33 | 0.72 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4181 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 784 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6JIZ · Apo structure of an imine reductase at 1.76 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 6JIZ · PDBe 6JIZ · UniProt D3Q3R0
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