3C7I: Growth factor receptor-bound protein 2

X-RAY crystal structure of the complex between the grb2-sh2 domain and a flexible ligand, FPTVN. Determined by X-ray diffraction at 1.7 Å resolution. Released 12 Aug 2008.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 992
Mol. weight: 14.26 kDa
Ligands: TVN
Released: 12 Aug 2008

Explore 3C7I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C7I contains 2 α-helices and 9 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	61	1	1
α-helix	67-75	9
β-strand	82	1	2
β-strand	83-87	5	1
β-strand	95-101	7	1
β-strand	104-110	7	1
β-strand	111-112	2	3
β-strand	118-119	2	3
β-strand	124-125	2	3
α-helix	128-134	7
β-strand	149	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Growth factor receptor-bound protein 2	A	protein	116	Homo sapiens	P62993 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3C7I_1 Growth factor receptor-bound protein 2 (chains A)
IEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLR
DGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPTYVQHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
TVN	N-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-valyl-L-asp…	C21 H32 N5 O9 P	1

Water and common crystallization additives (FMT) are not listed.

Primary citation

Ligand Preorganization May be Accompanied by Entropic Penalties in Protein-Ligand Interactions. Benfield, A.P., Teresk, M.G., Plake, H.R. et al. Angew Chem Int Ed Engl (2006) 118:6984-6989. DOI 10.1002/ange.200600844 · PubMed

Other PDB entries of the same protein (UniProt P62993 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ICG 1.15 Å, Grb2 SH2 domain in phosphopeptide free form
3WA4 1.35 Å, Grb2 SH2 domain/CD28-derived peptide complex
1JYR 1.55 Å, Xray Structure of Grb2 SH2 Domain Complexed with a Phosphorylated Peptide
2VWF 1.58 Å, Grb2 SH3C (2)
2VVK 1.6 Å, Grb2 SH3C (1)
3OV1 1.6 Å, Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide
4P9V 1.64 Å, Grb2 SH2 complexed with a pTyr-Ac6cN-Asn tripeptide
1GCQ 1.68 Å, Crystal structure of vav and GRB2 SH3 domains
2W0Z 1.7 Å, Grb2 SH3C (3)
3IN8 1.7 Å, Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pTyr-Ile-Asn-NH2…
3S8L 1.71 Å, Protein-Ligand Interactions: Thermodynamic Effects Associated with Increasing…
3S8N 1.71 Å, Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide

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