6WM1: Grb2 SH2 domain

Crystal structure of the Grb2 SH2 domain in complex with a tripeptide: Ac-pY-Ac6c-N-phenylpropyl. Determined by X-ray diffraction at 1.8 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,956
Mol. weight: 29.06 kDa
Ligands: CA
Released: 2 Sept 2020

Explore 6WM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WM1 contains 5 α-helices and 16 β-strands across 2 chains. 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: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	61	1	1
α-helix	67-76	10
β-strand	82-87	6	1
β-strand	95-101	7	1
β-strand	104-110	7	1
β-strand	111-112	2	2
β-strand	118-119	2	2
β-strand	125	1	2
α-helix	128-134	7
β-strand	149-150	2	1
α-helix	151-152	2

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	61-63	3	3
α-helix	67-75	9
β-strand	82-87	6	3
β-strand	95-101	7	3
β-strand	104-110	7	3
β-strand	111-112	2	4
β-strand	118-119	2	4
β-strand	125	1	4
α-helix	128-134	7
β-strand	149-150	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Growth factor receptor-bound protein 2	A, C	protein	117	Homo sapiens	P62993 (AlphaFold model)
Ace-ptr-02K-asn-pra	B, D	protein	5	synthetic construct

Sequence of entity 1 (A, C), FASTA

>6WM1_1 Growth factor receptor-bound protein 2 (chains A, C)
IEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLR
DGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPTYVQAHHHHHH

Sequence of entity 2 (B, D), FASTA

>6WM1_2 ACE-PTR-02K-ASN-PRA (chains B, D)
XYANX

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (CL, GOL) are not listed.

Primary citation

Some thermodynamic effects of varying nonpolar surfaces in protein-ligand interactions. Cramer, D.L., Cheng, B., Tian, J. et al. Eur J Med Chem (2020) 208:112771-112771. DOI 10.1016/j.ejmech.2020.112771 · 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…
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…

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