MolNFT v1 · #109579 · protein
GRB7 SH2 domain with phosphotyrosine mimetic inhibitor peptide
4X6S · Growth factor receptor-bound protein 7: “GRB7 SH2 domain with phosphotyrosine mimetic inhibitor peptide”. X-ray diffraction, 1 ligand (48V), 2 pockets (best druggability 0.41). MolNFT v1 #109579 on GenesisL1: 3D structure, binding…
- PDB
- 4X6S
- Type
- protein
- Length
- 233 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 7; Phosphotyrosine mimetic inhibitor peptide G7-TEM1
- UniProt
- Q14451
- Ligands
- 48V
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Growth factor receptor-bound protein 7 | protein | 106 | 18% helix, 33% strand | Q14451 |
| B | Growth factor receptor-bound protein 7 | protein | 107 | 18% helix, 33% strand | Q14451 |
| L, M | Phosphotyrosine mimetic inhibitor peptide G7-TEM1 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · 2 copies · chains A, L, M
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 | 111 | 0.41 | 0.76 | 23 | empty |
| 2 | 76 | 0.33 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–M · 519 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 518 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 487 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4X6S · Grb7 SH2 domain with phosphotyrosine mimetic inhibitor peptide · the same entry in another collection · chain A against A, 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 A 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 4X6S · PDBe 4X6S · UniProt Q14451
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