Research workbench
Crystal structure of ihhn bound to CDOFN3
Analyse Crystal structure of ihhn bound to CDOFN3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N1F
- Type
- protein
- Length
- 497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indian hedgehog protein; Cell adhesion molecule-RELATED/DOWN-regulated by oncogenes
- UniProt
- Q14623, Q4KMG0
- Ligands
- CA, ZN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indian hedgehog protein | protein | 151 | 28% helix, 21% strand | Q14623 |
| B | Indian hedgehog protein | protein | 150 | 27% helix, 21% strand | Q14623 |
| C | Cell adhesion molecule-RELATED/DOWN-regulated by oncogenes | protein | 94 | 3% helix, 50% strand | Q4KMG0 |
| D | Cell adhesion molecule-RELATED/DOWN-regulated by oncogenes | protein | 102 | 7% helix, 46% strand | Q4KMG0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.77 | 0.82 | 75 | empty |
| 2 | 171 | 0.51 | 0.78 | 27 | empty |
| 3 | 191 | 0.51 | 0.77 | 35 | empty |
| 4 | 74 | 0.38 | 0.78 | 17 | empty |
| 5 | 64 | 0.26 | 0.72 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–D · 710 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 294 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 284 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3N1F · Crystal Structure of IhhN bound to CDOFn3 · the same entry in another collection · chain D against D, TM-score 1.00
- Q14623 · AlphaFold monomer V2.0 prediction for indian hedgehog protein (Q14623) · a predicted model of the same protein · chain A 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 C 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 Q14623
- Every structure of UniProt Q4KMG0
- Elsewhere: RCSB PDB 3N1F · PDBe 3N1F · UniProt Q14623 · UniProt Q4KMG0
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