MolNFT v1 · #37070 · protein
Sad structure determination: crystal structure of the intrinsic dimerization SH3 domain of the IB1 scaffold protein
2FPD · C-jun-amino-terminal kinase interacting protein 1: “Sad structure determination: crystal structure of the intrinsic dimerization SH3 domain of the IB1 scaffold…”. X-ray diffraction, 2 ligands (GLC, SO4), 3 pockets (best druggability…
- PDB
- 2FPD
- Type
- protein
- Length
- 248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-jun-amino-terminal kinase interacting protein 1
- UniProt
- Q9R237
- Ligands
- GLC, SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | C-jun-amino-terminal kinase interacting protein 1 | protein | 62 | 5% helix, 44% strand | Q9R237 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.70 | 0.90 | 43 | empty |
| 2 | 134 | 0.44 | 0.76 | 20 | empty |
| 3 | 76 | 0.34 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 894 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 869 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 488 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 423 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 214 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2FPD · Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R237 · AlphaFold monomer V2.0 prediction for C-jun-amino-terminal kinase- interacting protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9R237
- Elsewhere: RCSB PDB 2FPD · PDBe 2FPD · UniProt Q9R237
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