MolNFT v1 · #95499 · protein
Crystal structure of a 3ALPHA-hydroxysteroid dehydrogenase (BAIA2) associated with secondary bile acid synthesis from clostridium scindens VPI12708 in complex with a putative NAD(+)-oh- adduct at 2.0 a resolution
4IS3 · Bile acid 3-alpha hydroxysteroid dehydrogenase: “Crystal structure of a 3ALPHA-hydroxysteroid dehydrogenase (BAIA2) associated with secondary bile acid…”. X-ray diffraction, 2 ligands (NAD, UNL), 13 pockets (best druggability 0.85).…
- PDB
- 4IS3
- Type
- protein
- Length
- 997 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bile acid 3-alpha hydroxysteroid dehydrogenase
- UniProt
- P19337
- Ligands
- NAD, UNL
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Bile acid 3-alpha hydroxysteroid dehydrogenase | protein | 249 | 51% helix, 15% strand | P19337 |
| C | Bile acid 3-alpha hydroxysteroid dehydrogenase | protein | 250 | 48% helix, 15% strand | P19337 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- UNL · Unknown ligand · ion · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.85 | 0.86 | 60 | empty |
| 2 | 465 | 0.75 | 0.84 | 53 | NAD, UNL |
| 3 | 416 | 0.73 | 0.84 | 52 | NAD, UNL |
| 4 | 491 | 0.73 | 0.82 | 52 | NAD, UNL |
| 5 | 447 | 0.73 | 0.83 | 51 | NAD, UNL |
Interfaces
6 interfaces between chains.
- A–B · 1753 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1745 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1251 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1246 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 4IS3 · Crystal structure of a 3alpha-hydroxysteroid dehydrogenase (BaiA2) associated with… · the same entry in another collection · chain D against D, TM-score 1.00
- P19337 · AlphaFold monomer V2.0 prediction for 3ALPHA-hydroxy bile acid-CoA- ester 3-dehydrogenase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P19337
- Elsewhere: RCSB PDB 4IS3 · PDBe 4IS3 · UniProt P19337
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