MolNFT v1 · #75460 · protein

GRB7 SH2 with peptide

3PQZ · Growth factor receptor-bound protein 7: “GRB7 SH2 with peptide”. X-ray diffraction, 3 pockets (best druggability 0.78). MolNFT v1 #75460 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PQZ
Type: protein
Length: 425 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Growth factor receptor-bound protein 7; Cyclic peptide
UniProt: Q14451
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 20% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Growth factor receptor-bound protein 7	protein	104	23% helix, 29% strand	Q14451
B	Growth factor receptor-bound protein 7	protein	105	19% helix, 29% strand	Q14451
C	Growth factor receptor-bound protein 7	protein	97	21% helix, 31% strand	Q14451
D	Growth factor receptor-bound protein 7	protein	97	20% helix, 34% strand	Q14451
L, M	Cyclic peptide	protein	11	0% helix, 0% strand	—

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1180	0.78	0.80	110	empty
2	103	0.36	0.74	22	empty
3	55	0.27	0.74	15	empty

Interfaces

11 interfaces between chains.

B–M · 484 Å² buried · 9 hydrogen bonds · protein-protein
A–L · 477 Å² buried · 9 hydrogen bonds · protein-protein
A–M · 236 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 234 Å² buried · 0 hydrogen bonds · protein-protein
B–L · 233 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

3PQZ · Grb7 SH2 with peptide · the same entry in another collection · chain M against M, 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 C against A, TM-score 0.98

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 3PQZ · PDBe 3PQZ · UniProt Q14451

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