MolNFT v1 · #72203 · protein
Crystal structure of dhhn bound to BOCFN3
3N1G · Desert hedgehog protein: “Crystal structure of dhhn bound to BOCFN3”. X-ray diffraction, 3 ligands (CA, ZN, MG), 3 pockets (best druggability 0.74). MolNFT v1 #72203 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3N1G
- Type
- protein
- Length
- 505 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desert hedgehog protein; Brother of cdo
- UniProt
- O43323, Q9BWV1
- Ligands
- CA, ZN, MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Desert hedgehog protein | protein | 151 | 27% helix, 18% strand | O43323 |
| C | Brother of cdo | protein | 104 | 7% helix, 46% strand | Q9BWV1 |
| D | Brother of cdo | protein | 99 | 3% helix, 45% strand | Q9BWV1 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.74 | 0.78 | 91 | empty |
| 2 | 247 | 0.53 | 0.77 | 38 | empty |
| 3 | 74 | 0.36 | 0.77 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–C · 729 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 728 Ų buried · 21 hydrogen bonds · protein-protein
- B–A · 328 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 195 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3N1G · Crystal structure of DhhN bound to BOCFn3 · the same entry in another collection · chain D against D, TM-score 1.00
- O43323 · AlphaFold monomer V2.0 prediction for desert hedgehog protein (O43323) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9BWV1 · AlphaFold monomer V2.0 prediction for brother of cdo (Q9BWV1) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 O43323
- Every structure of UniProt Q9BWV1
- Elsewhere: RCSB PDB 3N1G · PDBe 3N1G · UniProt O43323 · UniProt Q9BWV1
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