Growth factor receptor-bound protein 2
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 53–163 | Fragment：SH2 domain | FYI N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L-aspartamide × 2 FMT FORMIC ACID × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ligand in lyophilized powder form was dissolved in a 15.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1. 3.5 uL of this solution was mixed with 3.5 uL of 5.0 M sodium formate, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after six weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K | Resolution 1.70 Å R-free 0.211 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 3IN8 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1AZE NMR STRUCTURE OF THE COMPLEX BETWEEN THE C32S-Y7V MUTANT OF THE NSH3 DOMAIN OF GRB2 WITH A PEPTIDE FROM SOS, 10 STRUCTURES Deposited 1997-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–56（56 aa）
Fragment：N-TERMINAL SH3 DOMAIN, RESIDUES 1 - 55
|
Mutation：Y7V, C32S | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；293 K；Ionic strength (raw mmCIF value) NACL 100mM；Pressure 1
NMR sample composition
H2O, PHOSPHATE BUFFER 20MM, NACL 100MM
|
Resolution not provided |
| 1BMB GRB2-SH2 DOMAIN IN COMPLEX WITH KPFY*VNVEF (PKF270-974) Deposited 1998-07-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
46–168（123 aa）
Fragment：SH2 DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PROTEIN (15MG/ML IN 100MM SODIUM CHLORIDE, 0.02% SODIUM AZIDE) WAS CRYSTALLIZED FROM 46% SATURATED AMMONIUM SULFATE, 100MM SODIUM MES PH 6.5, IN PRESENCE OF A 2-FOLD EXCESS OF LIGAND
|
Resolution 1.80 Å R-free 0.218 |
| 1BMB GRB2-SH2 DOMAIN IN COMPLEX WITH KPFY*VNVEF (PKF270-974) Deposited 1998-07-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
46–168（123 aa）
Fragment：SH2 DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PROTEIN (15MG/ML IN 100MM SODIUM CHLORIDE, 0.02% SODIUM AZIDE) WAS CRYSTALLIZED FROM 46% SATURATED AMMONIUM SULFATE, 100MM SODIUM MES PH 6.5, IN PRESENCE OF A 2-FOLD EXCESS OF LIGAND
|
Resolution 1.80 Å R-free 0.218 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain B
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain D
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain F
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain H
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain I
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain J
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain K
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain L
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1FHS THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE SRC HOMOLOGY DOMAIN-2 OF THE GROWTH FACTOR RECEPTOR BOUND PROTEIN-2, NMR, 18 STRUCTURES Deposited 1997-06-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–163（111 aa）
Fragment：SH2 DOMAIN
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5.3；298 K
|
Resolution not provided |
| 1GCQ CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS Deposited 2000-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
159–217（59 aa）
Fragment：C-TERMINAL SH3 DOMAIN
Chain B
159–217（59 aa）
Fragment：C-TERMINAL SH3 DOMAIN
|
Not recorded | MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.2 K；2-methyl-2,4-pentanediol, imidazole, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K
|
Resolution 1.68 Å R-free 0.235 |
| 1GFC SOLUTION STRUCTURE AND LIGAND-BINDING SITE OF THE C-TERMINAL SH3 DOMAIN OF GRB2 Deposited 1994-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
159–215（57 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1GFD SOLUTION STRUCTURE AND LIGAND-BINDING SITE OF THE C-TERMINAL SH3 DOMAIN OF GRB2 Deposited 1994-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
159–215（57 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1GHU NMR solution structure of growth factor receptor-bound protein 2 (GRB2) SH2 domain, 24 structures Deposited 1996-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
60–158（99 aa）
Fragment：SH2 DOMAIN
|
Mutation：RESIDUES 58-59, 159-164 ARE CLONING ARTIFACTS | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.2；298 K
|
Resolution not provided |
| 1GRI GRB2 Deposited 1995-02-28 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–217（217 aa）
Chain B
1–217（217 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.10 Å |
| 1IO6 GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 (GRB2) C-TERMINAL SH3 DOMAIN COMPLEXED WITH A LIGAND PEPTIDE (NMR, MINIMIZED MEAN STRUCTURE) Deposited 2001-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
159–215（57 aa）
Fragment：C-TERMINAL SH3(RESIDUE 159-215)
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；298 K
|
Resolution not provided |
| 1JYR Xray Structure of Grb2 SH2 Domain Complexed with a Phosphorylated Peptide Deposited 2001-09-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
60–151（92 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；ammonium phosphate, PEG400, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.55 Å R-free 0.228 |
| 1JYR Xray Structure of Grb2 SH2 Domain Complexed with a Phosphorylated Peptide Deposited 2001-09-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
60–151（92 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；ammonium phosphate, PEG400, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.55 Å R-free 0.228 |
| 1JYU Xray Structure of Grb2 SH2 Domain Deposited 2001-09-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
60–151（92 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG4000, glycerol, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.75 Å R-free 0.287 |
| 1JYU Xray Structure of Grb2 SH2 Domain Deposited 2001-09-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
60–151（92 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG4000, glycerol, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.75 Å R-free 0.287 |
| 1QG1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN COMPLEXED WITH AN SHC-DERIVED PEPTIDE Deposited 1999-04-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
58–159（102 aa）
Fragment：SH2
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.3；301 K
|
Resolution not provided |
| 1X0N NMR structure of growth factor receptor binding protein SH2 domain complexed with the inhibitor Deposited 2005-03-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
58–159（102 aa）
Fragment：SH2 DOMAIN
|
Not recorded | DTF 4-[(10S,14S,18S)-18-(2-AMINO-2-OXOETHYL)-14-(1-NAPHTHYLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL]BENZYLPHOSPHONIC ACID × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.3；298 K；Pressure 1
NMR sample composition
1mM SH2 U-13C, 15N; 20mM sodium phosphate; 150mM NaCl | 90% H2O/10% D2O
|
Resolution not provided |
| 2AOA Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG3350, sodium chloride, sodium acetate, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.99 Å R-free 0.307 |
| 2AOA Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG3350, sodium chloride, sodium acetate, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.99 Å R-free 0.307 |
| 2AOA Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
Chain B
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 3 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG3350, sodium chloride, sodium acetate, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.99 Å R-free 0.307 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
Chain D
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
Chain B
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2H5K Crystal Structure of Complex Between the Domain-Swapped Dimeric Grb2 SH2 Domain and Shc-Derived Ligand, Ac-NH-pTyr-Val-Asn-NH2 Deposited 2006-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
53–162（110 aa）
Fragment：SH2 Domain
Chain B
53–162（110 aa）
Fragment：SH2 Domain
|
Not recorded | CAC CACODYLATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Protein-ligand solution in 25 mM sodium cacodylate, pH 6.0 mixed with equal volume of 0.1 M sodium cacodylate, 0.1 M calcium acetate, 18% PEG 8000, pH 6.0., VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.25 Å R-free 0.300 |
| 2HUW X-ray crystal structure of the Grb2 SH2 domain complexed to a constrained and cyclopropane-derived ligand Deposited 2006-07-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–162（110 aa）
Fragment：SH2 domain
|
Not recorded | YVN N-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-L-valyl-L-aspartamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Ligand (cpYVN) was added to a 1.5 molar excess to a solution of 50 mg/ml Grb2-SH2 in 50 mM sodium cacodylate at PH 6.0. This solution was mixed with an equal volume of 4% (v/v) PEG 400, 2.0 M (NH4)2PO4., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.227 |
| 2HUW X-ray crystal structure of the Grb2 SH2 domain complexed to a constrained and cyclopropane-derived ligand Deposited 2006-07-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
53–162（110 aa）
Fragment：SH2 domain
|
Not recorded | YVN N-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-L-valyl-L-aspartamide × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Ligand (cpYVN) was added to a 1.5 molar excess to a solution of 50 mg/ml Grb2-SH2 in 50 mM sodium cacodylate at PH 6.0. This solution was mixed with an equal volume of 4% (v/v) PEG 400, 2.0 M (NH4)2PO4., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.227 |
| 2VVK Grb2 SH3C (1) Deposited 2008-06-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
161–214（54 aa）
Fragment：SH3 DOMAIN, RESIDUES 161-214
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.6；8% PEG 4K, 0.1M NAACETATE PH 4.6
|
Resolution 1.60 Å R-free 0.178 |
| 2VWF Grb2 SH3C (2) Deposited 2008-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
159–214（56 aa）
Fragment：SH3 DOMAIN, RESIDUES 159-214
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；2M TRI-AMMONIUM CITRATE, 0.1M BIS-TRIS PROPANE PH7, pH 7.0
|
Resolution 1.58 Å R-free 0.219 |
| 2W0Z Grb2 SH3C (3) Deposited 2008-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
159–214（56 aa）
Fragment：SH3 DOMAIN, RESIDUES 159-214
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；0.7 M TRISODIUM CITRATE, 0.1 M TRIS PH 8.5
|
Resolution 1.70 Å R-free 0.206 |
| 3C7I X-RAY crystal structure of the complex between the grb2-sh2 domain and a flexible ligand, FPTVN. Deposited 2008-02-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–162（110 aa）
|
Not recorded | TVN N-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-valyl-L-aspartamide × 2 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；LIGAND (FPTVN) was added in a 1.5 molar excess to 15 MG/ML GRB2-SH2 in pure water.
This solution was mixed with an equal volume of 4.0 m sodium formate., pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293KK
|
Resolution 1.70 Å R-free 0.234 |
| 3IMD Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | FYQ N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 1 CL CHLORIDE ION × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.237 |
| 3IMD Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | FYQ N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.237 |
| 3IMD Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
Chain B
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | FYQ N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 2 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.237 |
| 3IMJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYI (1R,2S,3R,1S',1S")Phosphoric acid mono(4-{2-[1-(1,2-dicarbamoylethylcarbamoyl)-3-carbamoylpropylcarbamoyl]-3-methylcarbamoylcyclopropyl}phenyl) ester × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；Ligand in lyophilized powder form was dissolved in a 11.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4 uL of this solution was mixed with 3 uL of 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% v/v PEG MW4000, pH 4.6 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.229 |
| 3IMJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYI (1R,2S,3R,1S',1S")Phosphoric acid mono(4-{2-[1-(1,2-dicarbamoylethylcarbamoyl)-3-carbamoylpropylcarbamoyl]-3-methylcarbamoylcyclopropyl}phenyl) ester × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；Ligand in lyophilized powder form was dissolved in a 11.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4 uL of this solution was mixed with 3 uL of 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% v/v PEG MW4000, pH 4.6 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.229 |
| 3IMJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
Chain B
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYI (1R,2S,3R,1S',1S")Phosphoric acid mono(4-{2-[1-(1,2-dicarbamoylethylcarbamoyl)-3-carbamoylpropylcarbamoyl]-3-methylcarbamoylcyclopropyl}phenyl) ester × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；Ligand in lyophilized powder form was dissolved in a 11.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4 uL of this solution was mixed with 3 uL of 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% v/v PEG MW4000, pH 4.6 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.229 |
| 3IN7 Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYQ N~2~-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-D-glutaminyl-D-aspartamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.6 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1.7:1. 3.5 uL of this solution was mixed with 3.5 uL of 0.1 M HEPES, 20% w/v PEG MW10,000, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after two weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.250 |
| 3IN7 Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYQ N~2~-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-D-glutaminyl-D-aspartamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.6 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1.7:1. 3.5 uL of this solution was mixed with 3.5 uL of 0.1 M HEPES, 20% w/v PEG MW10,000, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after two weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.250 |
| 3IN7 Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
Chain C
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYQ N~2~-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-D-glutaminyl-D-aspartamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.6 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1.7:1. 3.5 uL of this solution was mixed with 3.5 uL of 0.1 M HEPES, 20% w/v PEG MW10,000, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after two weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.250 |
| 3KFJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-E-N-NH2 Tripeptide Mimic Deposited 2009-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain, residues 53-163
|
Not recorded | YEN N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-alpha-glutamyl-L-aspartamide × 1 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyophilized powder form was dissolved in a 9.5 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4uL of this solution was mixed with 3uL of 0.1 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.230 |
| 3KFJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-E-N-NH2 Tripeptide Mimic Deposited 2009-10-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain, residues 53-163
|
Not recorded | YEN N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-alpha-glutamyl-L-aspartamide × 2 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyophilized powder form was dissolved in a 9.5 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4uL of this solution was mixed with 3uL of 0.1 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.230 |
| 3MXC Structures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a Conformational Switch and Their Functional Implications. Deposited 2010-05-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
55–152（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
293 K；0.1 M Tris ,0.1M Bicine, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.244 |
| 3MXY Structures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a Conformational Switch and Their Functional Implications. Deposited 2010-05-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
55–152（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris ,0.1M Bicine, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.252 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
55–152（98 aa）
Fragment：SH2 domain
Chain C
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
52–162（111 aa）
Fragment：SH2 domain
Chain E
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | CL CHLORIDE ION × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
52–162（111 aa）
Fragment：SH2 domain
Chain D
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
52–162（111 aa）
Fragment：SH2 domain
Chain F
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N8M Crystal Structure of the Grb2 SH2 Domain in Complex with An Acyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：Grb2 SH2 domain, residues 55-153
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 12% v/v glycerol, 1.5 M ammonium sulfate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex after 8 weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.224 |
| 3N8M Crystal Structure of the Grb2 SH2 Domain in Complex with An Acyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
Fragment：Grb2 SH2 domain, residues 55-153
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 12% v/v glycerol, 1.5 M ammonium sulfate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex after 8 weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.224 |
| 3OV1 Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2010-09-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | GOL GLYCEROL × 2 FMT FORMIC ACID × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 20% w/v Polyethylene Glycol 10,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.214 |
| 3OV1 Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2010-09-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | GOL GLYCEROL × 4 FMT FORMIC ACID × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 20% w/v Polyethylene Glycol 10,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.214 |
| 3OVE Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2010-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M magnesium chloride hexahydrate, 0.1 M TRIS,30% w/v polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.82 Å R-free 0.260 |
| 3OVE Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2010-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M magnesium chloride hexahydrate, 0.1 M TRIS,30% w/v polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.82 Å R-free 0.260 |
| 3S8L Protein-Ligand Interactions: Thermodynamic Effects Associated with Increasing Hydrophobic Surface Area Deposited 2011-05-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | CL CHLORIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 3.5 M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.71 Å R-free 0.256 |
| 3S8N Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2011-05-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | GOL GLYCEROL × 3 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 4.3 M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.71 Å R-free 0.244 |
| 3S8N Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2011-05-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | GOL GLYCEROL × 6 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 4.3 M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.71 Å R-free 0.244 |
| 3S8O Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2011-05-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | NA SODIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 5.0 M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.85 Å R-free 0.201 |
| 3WA4 Grb2 SH2 domain/CD28-derived peptide complex Deposited 2013-04-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
60–152（93 aa）
Fragment：SH2 domain, UNP resideus 57-152
|
Not recorded | CD CADMIUM ION × 1 ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 1.25M sodium acetate, 0.1M cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.35 Å R-free 0.209 |
| 3WA4 Grb2 SH2 domain/CD28-derived peptide complex Deposited 2013-04-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
60–152（93 aa）
Fragment：SH2 domain, UNP resideus 57-152
|
Not recorded | CD CADMIUM ION × 1 ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 1.25M sodium acetate, 0.1M cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.35 Å R-free 0.209 |
| 4P9V Grb2 SH2 complexed with a pTyr-Ac6cN-Asn tripeptide Deposited 2014-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：UNP residues 53-163
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.2 M magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride, 30% w/v polyethylene glycol 4000
|
Resolution 1.64 Å R-free 0.257 |
| 4P9Z Grb2 SH2 complexed with a pTyr-Ac6c-Asn tripeptide Deposited 2014-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
|
Not recorded | GOL GLYCEROL × 1 ACT ACETATE ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, 30% w/v polyethylene glycol 4000
|
Resolution 1.80 Å R-free 0.239 |
| 4P9Z Grb2 SH2 complexed with a pTyr-Ac6c-Asn tripeptide Deposited 2014-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
|
Not recorded | GOL GLYCEROL × 2 ACT ACETATE ION × 4 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, 30% w/v polyethylene glycol 4000
|
Resolution 1.80 Å R-free 0.239 |
| 5CDW Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide Deposited 2015-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
54–153（100 aa）
Chain E
54–153（100 aa）
|
Mutation：W121G Mutation：W121G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.294 |
| 5CDW Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide Deposited 2015-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
54–153（100 aa）
Chain C
54–153（100 aa）
|
Mutation：W121G Mutation：W121G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.294 |
| 5CDW Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide Deposited 2015-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
54–153（100 aa）
Chain H
54–153（100 aa）
|
Mutation：W121G Mutation：W121G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.294 |
| 5CDW Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide Deposited 2015-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain K
54–153（100 aa）
Chain L
54–153（100 aa）
|
Mutation：W121G Mutation：W121G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.294 |
| 5CDW Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide Deposited 2015-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain O
54–153（100 aa）
Chain P
54–153（100 aa）
|
Mutation：W121G Mutation：W121G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.294 |
| 5CDW Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide Deposited 2015-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain U
54–153（100 aa）
Chain V
54–153（100 aa）
|
Mutation：W121G Mutation：W121G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.294 |
| 5CDW Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide Deposited 2015-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain Y
54–153（100 aa）
Chain Z
54–153（100 aa）
|
Mutation：W121G Mutation：W121G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.294 |
| 5CDW Crystal Structure Analysis of a mutant Grb2 SH2 domain (W121G) with a pYVNV peptide Deposited 2015-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain c
54–153（100 aa）
Chain d
54–153（100 aa）
|
Mutation：W121G Mutation：W121G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.294 |
| 6ICG Grb2 SH2 domain in phosphopeptide free form Deposited 2018-09-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
60–152（93 aa）
|
Not recorded | SO4 SULFATE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Sodium chloride, 0.1 M HEPES (pH 7.5), 1.6 M Ammonium sulfate
|
Resolution 1.15 Å R-free 0.169 |
| 6ICG Grb2 SH2 domain in phosphopeptide free form Deposited 2018-09-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
60–152（93 aa）
|
Not recorded | SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Sodium chloride, 0.1 M HEPES (pH 7.5), 1.6 M Ammonium sulfate
|
Resolution 1.15 Å R-free 0.169 |
| 6ICH Grb2 SH2 domain in domain swapped dimer form Deposited 2018-09-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
60–152（93 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES monohydrate (pH 6.5), 12% PEG 20,000
|
Resolution 2.00 Å R-free 0.242 |
| 6SDF N-terminal SH3 domain of Grb2 protein Deposited 2019-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–59（58 aa）
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M Hepes, 55% (v/v) MPD
|
Resolution 2.50 Å R-free 0.210 |
| 6SDF N-terminal SH3 domain of Grb2 protein Deposited 2019-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–59（58 aa）
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M Hepes, 55% (v/v) MPD
|
Resolution 2.50 Å R-free 0.210 |
| 6VK2 NMR solution structure of Grb2-SH2 domain at pH 7 Deposited 2020-01-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
55–150（96 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 138.2；Pressure 1
NMR sample composition
200 mM sodium chloride, 20 mM sodium phosphate, 1 mM EDTA, 1 mM PMSF, 5 mM sodium azide, 300 uM [U-100% 13C; U-100% 15N] Grb2-SH2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 6WM1 Crystal structure of the Grb2 SH2 domain in complex with a tripeptide: Ac-pY-Ac6c-N-phenylpropyl Deposited 2020-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；An aqueous solution containing a 1.5 molar ratio of ligand to protein, 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul precipitant solution containing 0.1 M HEPES, pH 7.5, and 25% w/v polyethylene glycol, MW 10,000, and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution at 298 K. Useable crystals grew after 4 weeks
|
Resolution 1.80 Å R-free 0.245 |
| 6WM1 Crystal structure of the Grb2 SH2 domain in complex with a tripeptide: Ac-pY-Ac6c-N-phenylpropyl Deposited 2020-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
53–163（111 aa）
Fragment：SH2 Domain
|
Not recorded | GOL GLYCEROL × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；An aqueous solution containing a 1.5 molar ratio of ligand to protein, 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul precipitant solution containing 0.1 M HEPES, pH 7.5, and 25% w/v polyethylene glycol, MW 10,000, and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution at 298 K. Useable crystals grew after 4 weeks
|
Resolution 1.80 Å R-free 0.245 |
| 6WO2 Crystal Structure of the Grb2 SH2 Domain in Complex with a Tripeptide: Ac-pY-Ac6c-N-isohexyl Deposited 2020-04-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 Domain
|
Not recorded | CA CALCIUM ION × 1 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；An aqueous solution containing a 1.5 molar ratio of ligand to protein, ca. 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul of a precipitant solution containing 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES, and 20% v/v 2-propanol (Hampton crystal screen I, condition no. 27), and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution. Usable crystals grew after 4 weeks
|
Resolution 2.00 Å R-free 0.275 |
| 6WO2 Crystal Structure of the Grb2 SH2 Domain in Complex with a Tripeptide: Ac-pY-Ac6c-N-isohexyl Deposited 2020-04-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
53–163（111 aa）
Fragment：SH2 Domain
|
Not recorded | IPA ISOPROPYL ALCOHOL × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；An aqueous solution containing a 1.5 molar ratio of ligand to protein, ca. 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul of a precipitant solution containing 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES, and 20% v/v 2-propanol (Hampton crystal screen I, condition no. 27), and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution. Usable crystals grew after 4 weeks
|
Resolution 2.00 Å R-free 0.275 |
| 7MPH GRB2 SH2 Domain with Compound 7 Deposited 2021-05-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
59–152（94 aa）
Chain E
59–152（94 aa）
Chain F
59–152（94 aa）
|
Not recorded | ZLY (4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid × 3 EDO 1,2-ETHANEDIOL × 7 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；12.4mg/mL GRB2 SH2 domain, 0.1mM Bis-Tris pH 5.5, 2M Ammonium Sulphate
|
Resolution 2.00 Å R-free 0.277 |
| 7MPH GRB2 SH2 Domain with Compound 7 Deposited 2021-05-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain B
59–152（94 aa）
Chain C
59–152（94 aa）
Chain D
59–152（94 aa）
|
Not recorded | ZLY (4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid × 3 EDO 1,2-ETHANEDIOL × 6 SO4 SULFATE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；12.4mg/mL GRB2 SH2 domain, 0.1mM Bis-Tris pH 5.5, 2M Ammonium Sulphate
|
Resolution 2.00 Å R-free 0.277 |
| 9I3P CryoEM structure of the Themis:Grb2 complex with bound ProMacrobody 256 Deposited 2025-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–217（217 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；25 mM Tris pH8, 100 mM NaCl, 2 mM DTT with added 8 mM CHAPSO for cryogrid sample preparation
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM GP2, 5 s blotting time
|
Resolution 3.30 Å |
| 9IAZ CryoEM structure of the Themis:Grb2 complex with bound ProMacrobody 256, local refinement Deposited 2025-02-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–217（217 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；25 mM Tris pH8, 100 mM NaCl, 2 mM DTT with added 8 mM CHAPSO for cryogrid sample preparation
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM GP2, 5 s blotting time
|
Resolution 3.20 Å |
| 9UOU Crystal structure of the fusion protein of T-lineage protein Themis and adaptor protein Grb2 Deposited 2025-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
158–214（57 aa）
Chain B
158–214（57 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M Tris-HCl pH 8.5, 2% (v/v) Tacsimate pH 8.0, 16% (w/v) polyethylene glycol 3350
|
Resolution 3.06 Å R-free 0.302 |
50 other PDB entries and 103 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | GRB2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–111； UniProt 53–163 |
