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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
- 2AOA
- Type
- protein
- Length
- 170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 2
- UniProt
- P62993
- Ligands
- S1S
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Growth factor receptor-bound protein 2 | protein | 93 | 17% helix, 26% strand | P62993 |
| B | Growth factor receptor-bound protein 2 | protein | 77 | 14% helix, 25% 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 · 3 copies · chains A, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A, B
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 | 117 | 0.46 | 0.78 | 23 | empty |
| 2 | 60 | 0.32 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1970 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2AOA · 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 2AOA · PDBe 2AOA · UniProt P62993
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