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Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the GRB2 SH2 domain
Analyse Crystal structures of a high-affinity macrocyclic peptide mimetic in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AOB
- Type
- protein
- Length
- 378 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 2
- UniProt
- P62993
- Ligands
- S1S
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Growth factor receptor-bound protein 2 | protein | 96 | 20% helix, 27% strand | P62993 |
| B, D | Growth factor receptor-bound protein 2 | protein | 93 | 17% helix, 28% strand | P62993 |
Ligands and binding sites
- S1S · 2-(4-((9S,10S,14S,Z)-18-(2-amino-2-oxoethyl)-9-(carboxymethyl)-14-(naphthalen-1-ylmethyl)-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl)phenyl)malonic acid · ligand · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.71 | 0.89 | 30 | empty |
| 2 | 529 | 0.68 | 0.78 | 65 | empty |
| 3 | 60 | 0.37 | 0.79 | 12 | empty |
| 4 | 57 | 0.30 | 0.76 | 17 | empty |
| 5 | 60 | 0.28 | 0.73 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2343 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2342 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 356 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 276 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2AOB · Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the… · the same entry in another collection · chain A against A, 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 0.68
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 2AOB · PDBe 2AOB · UniProt P62993
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