MolNFT v1 · #98365 · protein
Three dimensional structure of mutant D78A of human hd domain- containing protein 2, genomics consortium (nesg) target HR6723
4L7E · Hd domain-containing protein 2: “Three dimensional structure of mutant D78A of human hd domain- containing protein 2, genomics consortium…”. X-ray diffraction, 2 ligands (UNL, CL), 4 pockets (best druggability 0.63). MolNFT v1…
- PDB
- 4L7E
- Type
- protein
- Length
- 379 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hd domain-containing protein 2
- UniProt
- Q7Z4H3
- Ligands
- UNL, CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hd domain-containing protein 2 | protein | 187 | 71% helix, 1% strand | Q7Z4H3 |
| B | Hd domain-containing protein 2 | protein | 192 | 69% helix, 1% strand | Q7Z4H3 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 8 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 | 388 | 0.63 | 0.78 | 36 | CL, UNL |
| 2 | 387 | 0.63 | 0.78 | 36 | CL, UNL |
| 3 | 219 | 0.50 | 0.76 | 31 | empty |
| 4 | 67 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2381 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered, phosphorylation).
Compared structures
- 4L7E · Three dimensional structure of mutant D78A of human HD domain-containing protein 2… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7Z4H3 · AlphaFold monomer V2.0 prediction for 5'-deoxynucleotidase HDDC2 (Q7Z4H3) · 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 Q7Z4H3
- Elsewhere: RCSB PDB 4L7E · PDBe 4L7E · UniProt Q7Z4H3
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