3IN8: Grb2 SH2 Domain

Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic. Determined by X-ray diffraction at 1.7 Å resolution. Released 17 Nov 2009.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 988
Mol. weight: 14.35 kDa
Ligands: FYI
Released: 17 Nov 2009

Explore 3IN8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3IN8 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	104-109	6	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	117	Homo sapiens	P62993 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3IN8_1 Growth factor receptor-bound protein 2 (chains A)
IEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLR
DGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPTYVQAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
FYI	N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L…	C22 H34 N5 O9 P	1

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

Primary citation

Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization. Delorbe, J.E., Clements, J.H., Teresk, M.G. et al. J Am Chem Soc (2009) 131:16758-16770. DOI 10.1021/ja904698q · 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)
3C7I 1.7 Å, X-RAY crystal structure of the complex between the grb2-sh2 domain and a flexible…
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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