Research workbench
Crystal structure of the second SH3 domain of ITSN1 bound with a synthetic peptide
Analyse Crystal structure of the second SH3 domain of ITSN1 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
- 4IIM
- Type
- protein
- Length
- 141 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intersectin-1; Peptide ligand
- UniProt
- Q15811
- Ligands
- UNX
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intersectin-1 | protein | 57 | 5% helix, 54% strand | Q15811 |
| C, D | Peptide ligand | protein | 12 | 33% helix, 0% strand | — |
| B | Intersectin-1 | protein | 55 | 5% helix, 55% strand | Q15811 |
| E | Peptide ligand | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 11 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- B–D · 471 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 470 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 196 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 142 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4IIM · Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide · the same entry in another collection · chain C against C, TM-score 1.00
- Q15811 · AlphaFold monomer V2.0 prediction for intersectin-1 (Q15811) · a predicted model of the same protein · chain B 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 Q15811
- Elsewhere: RCSB PDB 4IIM · PDBe 4IIM · UniProt Q15811
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