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Crystal structure of the GRB2 SH2 domain in complex with a 20-membered macrocyclic ligand having the sequence pyvnv
Analyse Crystal structure of the GRB2 SH2 domain in complex with a 20-membered… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N7Y
- Type
- protein
- Length
- 306 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 2; 20-membered peptide-like macrocyclic ligand
- UniProt
- P62993
- Ligands
- 011
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Growth factor receptor-bound protein 2 | protein | 98 | 16% helix, 29% strand | P62993 |
| D, E, F | 20-membered peptide-like macrocyclic ligand | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 011 · 7-aminoheptanoic acid · ligand · 3 copies · chains D, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.35 | 0.78 | 14 | empty |
| 2 | 73 | 0.30 | 0.73 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–E · 394 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 391 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 387 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 163 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 154 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 3 modified (covalent ligand, phosphorylation).
Compared structures
- 3N7Y · Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand… · the same entry in another collection · chain C against C, TM-score 1.00
- P62993 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 2 (P62993) · a predicted model of the same protein · chain A 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 P62993
- Elsewhere: RCSB PDB 3N7Y · PDBe 3N7Y · UniProt P62993
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