Research workbench
Crystal structure of human 17BETA-hydroxysteroid dehydrogenase type 5 (AKR1C3) in complex with NADP+ and 2'-desmethyl-indomethacin
Analyse Crystal structure of human 17BETA-hydroxysteroid dehydrogenase type 5 (AKR1C3)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DBW
- Type
- protein
- Length
- 633 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldo-keto reductase family 1 member C3
- EC
- 1.1.1.213, 1.1.1.112, 1.1.1.188, 1.1.1.63, 1.1.1.64, 1.3.1.20
- UniProt
- P42330
- Ligands
- 511, NAP
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldo-keto reductase family 1 member C3 (EC 1.1.1.213, 1.1.1.112, 1.1.1.188, 1.1.1.63, 1.1.1.64, 1.3.1.20) | protein | 315 | 41% helix, 17% strand | P42330 |
| B | Aldo-keto reductase family 1 member C3 (EC 1.1.1.213, 1.1.1.112, 1.1.1.188, 1.1.1.63, 1.1.1.64, 1.3.1.20) | protein | 318 | 42% helix, 17% strand | P42330 |
Ligands and binding sites
- 511 · [1-(4-chlorobenzoyl)-5-methoxy-1H-indol-3-yl]acetic acid · ligand · 4 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.79 | 0.85 | 54 | NAP, 511 |
| 2 | 1103 | 0.78 | 0.80 | 112 | NAP, 511 |
| 3 | 65 | 0.34 | 0.77 | 18 | empty |
| 4 | 66 | 0.32 | 0.75 | 20 | empty |
| 5 | 72 | 0.30 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 372 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4DBW · Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 (AKR1C3) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P42330 · AlphaFold monomer V2.0 prediction for aldo-keto reductase family 1 member C3 (P42330) · a predicted model of the same protein · chain B 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 P42330
- Elsewhere: RCSB PDB 4DBW · PDBe 4DBW · UniProt P42330
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