Macromolecule Content

Total Structure Weight: 28.52 kDa
Atom Count: 1870
Residue Count: 199
Unique protein chains: 1

2HUW

X-ray crystal structure of the Grb2 SH2 domain complexed to a constrained and cyclopropane-derived ligand

DOI: 10.2210/pdb2HUW/pdb

Classification: HORMONE/GROWTH FACTOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-07-27 Released: 2006-08-15
Deposition Author(s): Benfield, A.P., Martin, S.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.227
R-Value Work: 0.195
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Ligand Preorganization May Be Accompanied by Entropic Penalties in Protein-Ligand Interactions.

Benfield, A.P., Teresk, M.G., Plake, H.R., Delorbe, J.E., Millspaugh, L.E., Martin, S.F.

(2006) Angew Chem Int Ed Engl 45: 6830-6835

PubMed: 17001728 Search on PubMed
DOI: 10.1002/anie.200600844
Primary Citation of Related Structures:
3C7I, 2HUW

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth factor receptor-bound protein 2	A, B	116	Homo sapiens	Mutation(s): 0 Gene Names: GRB2, ASH
Find proteins for P62993 (Homo sapiens) Explore P62993 Go to UniProtKB: P62993
NIH Common Fund Data Resources
PHAROS: P62993 GTEx: ENSG00000177885
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YVN Query on YVN Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain E [B] MOL2 format, chain C [A] MOL2 format, chain E [B]	A, B	N-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-L-valyl-L-aspartamide C₂₁ H₃₀ N₅ O₉ P LVYNAUCEOQBVSW-RDDKANTKSA-N		Ligand Interaction
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [B] MOL2 format, chain D [B]	B	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
YVN	Ka: 1000000 M^-1 Binding MOAD

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.227
R-Value Work: 0.195
R-Value Observed: 0.227
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.824	α = 90
b = 85.49	β = 92.6
c = 41.436	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Deposited Date: 2006-07-27
Released Date: 2006-08-15

Deposition Author(s):

Benfield, A.P.

Martin, S.F.

Revision History

Version 1.0: 2006-08-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description

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Deposit Data

Deposition Help & Resources

174994 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

2HUW

X-ray crystal structure of the Grb2 SH2 domain complexed to a constrained and cyclopropane-derived ligand

Ligand Preorganization May Be Accompanied by Entropic Penalties in Protein-Ligand Interactions.

Entity ID: 1

NIH Common Fund Data Resources

Protein Feature View

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Experimental Data

Structure Validation

Deposition Data

Revision History