Research workbench
Crystal structure of the second SH3 domain of ITSN2 bound with a synthetic peptide
Analyse Crystal structure of the second SH3 domain of ITSN2 bound with a synthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IIO
- Type
- protein
- Length
- 132 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intersectin-2; Synthetic peptide
- UniProt
- Q9NZM3
- Ligands
- ACE, UNX, CL, SO4
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intersectin-2 | protein | 63 | 5% helix, 51% strand | Q9NZM3 |
| B | Intersectin-2 | protein | 57 | 5% helix, 54% strand | Q9NZM3 |
| C | Synthetic peptide | protein | 12 | 42% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains C
- UNX · Unknown atom or ion · ion · 15 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.45 | 0.77 | 27 | UNX |
Interfaces
2 interfaces between chains.
- B–C · 507 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 166 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4IIO · Crystal Structure of the Second SH3 Domain of ITSN2 Bound with a Synthetic Peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZM3 · AlphaFold monomer V2.0 prediction for intersectin-2 (Q9NZM3) · a predicted model of the same protein · chain B 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 Q9NZM3
- Elsewhere: RCSB PDB 4IIO · PDBe 4IIO · UniProt Q9NZM3
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