Research workbench
GRB7 SH2 with bicyclic peptide containing py mimetic
Analyse GRB7 SH2 with bicyclic peptide containing py mimetic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TYI
- Type
- protein
- Length
- 443 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 7; Peptide inhibitor
- UniProt
- Q14451
- Ligands
- 99Y, 48V
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Growth factor receptor-bound protein 7 | protein | 104 | 19% helix, 27% strand | Q14451 |
| B | Growth factor receptor-bound protein 7 | protein | 105 | 21% helix, 29% strand | Q14451 |
| C | Growth factor receptor-bound protein 7 | protein | 104 | 18% helix, 31% strand | Q14451 |
| D | Growth factor receptor-bound protein 7 | protein | 102 | 22% helix, 29% strand | Q14451 |
| L, M, N, P | Peptide inhibitor | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- 99Y · 4-carboxy-D-phenylalanine · ligand · 4 copies · chains A, L, B, M, P, C, N, D
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · 4 copies · chains A, C, L, N, B, M, D, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.73 | 0.77 | 89 | 48V |
| 2 | 66 | 0.49 | 0.85 | 17 | 99Y |
| 3 | 71 | 0.43 | 0.81 | 16 | 99Y |
| 4 | 62 | 0.43 | 0.82 | 15 | 99Y |
Interfaces
14 interfaces between chains.
- C–D · 550 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 7 hydrogen bonds · protein-protein
- D–P · 376 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 375 Ų buried · 8 hydrogen bonds · protein-protein
- C–N · 363 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent, 4 isopeptide (covalent ligand, isopeptide).
Compared structures
- 5TYI · Grb7 SH2 with bicyclic peptide containing pY mimetic · the same entry in another collection · chain P against P, TM-score 1.00
- Q14451 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 7 (Q14451) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q14451
- Elsewhere: RCSB PDB 5TYI · PDBe 5TYI · UniProt Q14451
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