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Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with the fourth SH3 domain of ITSN1 (SH3d)
Analyse Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GBU
- Type
- protein
- Length
- 473 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.44
- Source
- Homo sapiens
- Molecule
- F-BAR and double SH3 domains protein 2; Intersectin-1
- UniProt
- O94868, Q15811
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · resolution 3.44 · 5 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | F-BAR and double SH3 domains protein 2 | protein | 62 | 5% helix, 45% strand | O94868 |
| B, F, H | Intersectin-1 | protein | 63 | 5% helix, 48% strand | Q15811 |
| D | Intersectin-1 | protein | 64 | 5% helix, 47% strand | Q15811 |
| E | F-BAR and double SH3 domains protein 2 | protein | 42 | 0% helix, 33% strand | O94868 |
| G | F-BAR and double SH3 domains protein 2 | protein | 54 | 6% helix, 43% strand | O94868 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.65 | 0.78 | 38 | empty |
| 2 | 107 | 0.40 | 0.75 | 19 | empty |
| 3 | 57 | 0.37 | 0.79 | 16 | empty |
| 4 | 60 | 0.33 | 0.76 | 14 | empty |
| 5 | 50 | 0.24 | 0.73 | 12 | empty |
Interfaces
12 interfaces between chains.
- C–D · 690 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 659 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 548 Ų buried · 3 hydrogen bonds · protein-protein
- H–E · 358 Ų buried · 1 hydrogen bond · protein-protein
- E–G · 306 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6GBU · Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with the fourth… · the same entry in another collection · chain H against H, TM-score 1.00
- O94868 · AlphaFold monomer V2.0 prediction for F-bar and double SH3 domains protein 2 (O94868) · a predicted model of the same protein · chain E against A, TM-score 0.95
- Q15811 · AlphaFold monomer V2.0 prediction for intersectin-1 (Q15811) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 O94868
- Every structure of UniProt Q15811
- Elsewhere: RCSB PDB 6GBU · PDBe 6GBU · UniProt O94868 · UniProt Q15811
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