MolNFT v1 · #116006 · protein

GRB7 SH2 with inhibitor peptide

5D0J · Growth factor receptor-bound protein 7: “GRB7 SH2 with inhibitor peptide”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.46). MolNFT v1 #116006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5D0J
Type: protein
Length: 434 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Growth factor receptor-bound protein 7; G7-tedfp peptide
UniProt: Q14451
Ligands: PO4
Pockets: 5 · best druggability 0.46

Structure

x-ray diffraction · 6 distinct chains · 18% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Growth factor receptor-bound protein 7	protein	106	16% helix, 33% strand	Q14451
B	Growth factor receptor-bound protein 7	protein	107	20% helix, 31% strand	Q14451
C	Growth factor receptor-bound protein 7	protein	102	17% helix, 36% strand	Q14451
D	Growth factor receptor-bound protein 7	protein	104	21% helix, 29% strand	Q14451
L	G7-tedfp peptide	protein	7	0% helix, 0% strand	—
M	G7-tedfp peptide	protein	8	0% helix, 0% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, L, D, M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	227	0.46	0.73	33	empty
2	69	0.36	0.77	21	empty
3	62	0.35	0.77	24	empty
4	71	0.29	0.72	17	empty
5	61	0.26	0.72	14	empty

Interfaces

6 interfaces between chains.

A–B · 467 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 433 Å² buried · 4 hydrogen bonds · protein-protein
D–M · 432 Å² buried · 11 hydrogen bonds · protein-protein
A–L · 296 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 233 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5D0J · Grb7 SH2 with inhibitor 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 D 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 5D0J · PDBe 5D0J · UniProt Q14451

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