MolNFT v1 · #123339 · protein
Crystal structure of maize AKR4C13 in P21 space group
5JGY · Aldose reductase, AKR4C13: “Crystal structure of maize AKR4C13 in P21 space group”. X-ray diffraction, 1 ligand (6KB), 4 pockets (best druggability 0.83). MolNFT v1 #123339 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5JGY
- Type
- protein
- Length
- 617 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldose reductase, AKR4C13
- UniProt
- E9JVD4
- Ligands
- 6KB
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldose reductase, AKR4C13 | protein | 307 | 42% helix, 15% strand | E9JVD4 |
| B | Aldose reductase, AKR4C13 | protein | 310 | 42% helix, 15% strand | E9JVD4 |
Ligands and binding sites
- 6KB · 4-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxybutanoic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.83 | 0.84 | 114 | 6KB, EDO |
| 2 | 295 | 0.71 | 0.85 | 47 | 6KB, EDO |
| 3 | 111 | 0.54 | 0.83 | 18 | EDO |
| 4 | 56 | 0.31 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 852 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5JGY · Crystal structure of maize AKR4C13 in P21 space group · 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 5JGY · PDBe 5JGY · UniProt E9JVD4
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