MolNFT v1 · #66284 · protein
The crystal structure of human haloacid dehalogenase-like hydrolase domain containing 2 (HDHD2)
3HLT: “The crystal structure of human haloacid dehalogenase-like hydrolase domain containing 2 (HDHD2)”. X-ray diffraction, 3 ligands (NA, SO4, CL), 7 pockets (best druggability 0.61). MolNFT v1 #66284 on GenesisL1: 3D structure, binding…
- PDB
- 3HLT
- Type
- protein
- Length
- 499 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDHD2
- UniProt
- Q9H0R4
- Ligands
- NA, SO4, CL
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDHD2 | protein | 256 | 39% helix, 20% strand | Q9H0R4 |
| C | HDHD2 | protein | 243 | 39% helix, 20% strand | Q9H0R4 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.61 | 0.75 | 45 | SO4, NA |
| 2 | 304 | 0.61 | 0.79 | 43 | empty |
| 3 | 236 | 0.60 | 0.80 | 26 | empty |
| 4 | 74 | 0.47 | 0.82 | 23 | empty |
| 5 | 162 | 0.42 | 0.74 | 24 | SO4, NA |
Interfaces
1 interface between chains.
- A–C · 276 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HLT · The crystal structure of human haloacid dehalogenase-like hydrolase domain containing 2… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H0R4 · AlphaFold monomer V2.0 prediction for haloacid dehalogenase-like hydrolase… · a predicted model of the same protein · chain A 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 Q9H0R4
- Elsewhere: RCSB PDB 3HLT · PDBe 3HLT · UniProt Q9H0R4
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