Research workbench
Crystal structure of maize AKR4C13 in complex with NADP and acetate
Analyse Crystal structure of maize AKR4C13 in complex with NADP and acetate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JGW
- Type
- protein
- Length
- 1,236 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldose reductase, AKR4C13
- UniProt
- E9JVD4
- Ligands
- NAP
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldose reductase, AKR4C13 | protein | 314 | 41% helix, 15% strand | E9JVD4 |
| B, D | Aldose reductase, AKR4C13 | protein | 307 | 42% helix, 15% strand | E9JVD4 |
| C | Aldose reductase, AKR4C13 | protein | 308 | 42% helix, 15% strand | E9JVD4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.87 | 0.88 | 130 | NAP |
| 2 | 892 | 0.86 | 0.88 | 99 | NAP, ACT |
| 3 | 270 | 0.73 | 0.87 | 47 | empty |
| 4 | 342 | 0.70 | 0.83 | 46 | NAP, ACT |
| 5 | 342 | 0.70 | 0.83 | 45 | NAP, ACT |
Interfaces
6 interfaces between chains.
- A–B · 862 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 857 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 331 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 265 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5JGW · Crystal structure of maize AKR4C13 in complex with NADP and acetate · 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 E9JVD4
- Elsewhere: RCSB PDB 5JGW · PDBe 5JGW · UniProt E9JVD4
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