MolNFT v1 · #72213 · protein
Crystal structure of dhhn bound to CDOFN3
3N1Q · Desert hedgehog protein: “Crystal structure of dhhn bound to CDOFN3”. X-ray diffraction, 2 ligands (CA, ZN), 9 pockets (best druggability 0.69). MolNFT v1 #72213 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3N1Q
- Type
- protein
- Length
- 713 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desert hedgehog protein; Cell adhesion molecule-RELATED/DOWN-regulated by oncogenes
- UniProt
- O43323, Q4KMG0
- Ligands
- CA, ZN
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Desert hedgehog protein | protein | 151 | 26% helix, 20% strand | O43323 |
| C, D, F | Cell adhesion molecule-RELATED/DOWN-regulated by oncogenes | protein | 87 | 0% helix, 52% strand | Q4KMG0 |
| E | Desert hedgehog protein | protein | 150 | 23% helix, 21% strand | O43323 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains B, A, D, E
- ZN · Zinc ion · metal · 3 copies · chains B, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.69 | 0.77 | 61 | ZN |
| 2 | 401 | 0.64 | 0.78 | 30 | empty |
| 3 | 509 | 0.62 | 0.75 | 45 | empty |
| 4 | 231 | 0.53 | 0.77 | 37 | empty |
| 5 | 136 | 0.52 | 0.80 | 26 | empty |
Interfaces
8 interfaces between chains.
- A–D · 706 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 704 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 704 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 402 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 319 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3N1Q · Crystal Structure of DhhN bound to CDOFn3 · the same entry in another collection · chain F against F, TM-score 1.00
- O43323 · AlphaFold monomer V2.0 prediction for desert hedgehog protein (O43323) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q4KMG0 · AlphaFold monomer V2.0 prediction for cell adhesion molecule- RELATED/DOWN-regulated by… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q4KMG0
- Elsewhere: RCSB PDB 3N1Q · PDBe 3N1Q · UniProt O43323 · UniProt Q4KMG0
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