MolNFT v1 · #69614 · protein
Crystal structure of the catalytic domain of human hydroxysteroid dehydrogenase like 2 (HSDL2)
3KVO · Hydroxysteroid dehydrogenase-like protein 2: “Crystal structure of the catalytic domain of human hydroxysteroid dehydrogenase like 2 (HSDL2)”. X-ray diffraction, 1 ligand (NAP), 2 pockets (best druggability 0.77). MolNFT v1 #69614…
- PDB
- 3KVO
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxysteroid dehydrogenase-like protein 2
- EC
- 1.-.-.-
- UniProt
- Q6YN16
- Ligands
- NAP
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxysteroid dehydrogenase-like protein 2 (EC 1.-.-.-) | protein | 273 | 42% helix, 15% strand | Q6YN16 |
| B | Hydroxysteroid dehydrogenase-like protein 2 (EC 1.-.-.-) | protein | 276 | 44% helix, 14% strand | Q6YN16 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.77 | 0.83 | 50 | NAP |
| 2 | 615 | 0.77 | 0.83 | 62 | NAP |
Interfaces
1 interface between chains.
- A–B · 1685 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3KVO · Crystal structure of the catalytic domain of human Hydroxysteroid dehydrogenase like 2… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6YN16 · AlphaFold monomer V2.0 prediction for hydroxysteroid dehydrogenase- like protein 2… · 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 Q6YN16
- Elsewhere: RCSB PDB 3KVO · PDBe 3KVO · UniProt Q6YN16
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