1m5i

Crystal Structure of the coiled coil region 129-250 of the tumor suppressor gene product APC

Method: X-RAY DIFFRACTION D_max: 85.0 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

APC protein

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 126–250	Fragment：coiled-coil region	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；16% PEG 3350, 100mM potassium iodide, 10mM strontium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.309

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 1M5I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DEB CRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC Deposited 1999-11-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–55（54 aa） Fragment：N-TERMINAL COILED COIL DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；15% PEG 4000, 0.1M AMMONIUM ACETATE, 0.1M NA ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.277
1DEB CRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC Deposited 1999-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–55（54 aa） Fragment：N-TERMINAL COILED COIL DOMAIN	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；15% PEG 4000, 0.1M AMMONIUM ACETATE, 0.1M NA ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.277
1DEB CRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC Deposited 1999-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–55（54 aa） Fragment：N-TERMINAL COILED COIL DOMAIN Chain B 2–55（54 aa） Fragment：N-TERMINAL COILED COIL DOMAIN	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；15% PEG 4000, 0.1M AMMONIUM ACETATE, 0.1M NA ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.277
1DEB CRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC Deposited 1999-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–55（54 aa） Fragment：N-TERMINAL COILED COIL DOMAIN Chain B 2–55（54 aa） Fragment：N-TERMINAL COILED COIL DOMAIN	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；15% PEG 4000, 0.1M AMMONIUM ACETATE, 0.1M NA ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.277
1DEB CRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC Deposited 1999-11-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–55（54 aa） Fragment：N-TERMINAL COILED COIL DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；15% PEG 4000, 0.1M AMMONIUM ACETATE, 0.1M NA ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.277
1EMU STRUCTURE OF THE AXIN RGS-HOMOLOGOUS DOMAIN IN COMPLEX WITH A SAMP REPEAT FROM APC Deposited 2000-03-17	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 B 2034–2049（16 aa） Fragment：THIRD SAMP REPEAT	Not recorded	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；MES, PEG 400, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.221
1JPP The Structure of a beta-Catenin Binding Repeat from Adenomatous Polyposis Coli (APC) in Complex with beta-Catenin Deposited 2001-08-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1021–1035（15 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；PEG 8000, sodium potassium phosphate, sodium chloride, DTT, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.274
1JPP The Structure of a beta-Catenin Binding Repeat from Adenomatous Polyposis Coli (APC) in Complex with beta-Catenin Deposited 2001-08-02	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 D 1021–1035（15 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；PEG 8000, sodium potassium phosphate, sodium chloride, DTT, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.274
1T08 Crystal structure of beta-catenin/ICAT helical domain/unphosphorylated APC R3 Deposited 2004-04-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1484–1498（15 aa） Fragment：repeat 3 (RESIDUES 1484-1498)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；297 K；PEG3400, Potassium phosphate, pH 6.5, EVAPORATION, temperature 297K	Resolution 2.10 Å R-free 0.241
1TH1 Beta-catenin in complex with a phosphorylated APC 20aa repeat fragment Deposited 2004-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1362–1540（179 aa） Fragment：phosphorylated 20 amino acid repeat	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Tris, sidium chloride, PEG2000MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.257
1TH1 Beta-catenin in complex with a phosphorylated APC 20aa repeat fragment Deposited 2004-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1362–1540（179 aa） Fragment：phosphorylated 20 amino acid repeat	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Tris, sidium chloride, PEG2000MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.257
1V18 The crystal structure of beta-catenin armadillo repeat complexed with a phosphorylated APC 20mer repeat. Deposited 2004-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1482–1528（47 aa） Fragment：RESIDUES 1482-1528	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.10 Å R-free 0.253
2RQU Solution structure of the complex between the DDEF1 SH3 domain and the APC SAMP1 motif Deposited 2009-12-14	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1578–1596（19 aa） Fragment：UNP residues 1578-1596	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；278 K；Pressure ambient NMR sample composition 0.5 mM [U-15N] DDEF1 SH3-1, 0.5 mM [U-15N] APC SAMP1-2, 5 mM sodium phosphate-3, 5 mM [U-2H] DTT-4, 0.02 % sodium azide-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] DDEF1 SH3-6, 0.5 mM [U-13C; U-15N] APC SAMP1-7, 5 mM sodium phosphate-8, 5 mM [U-2H] DTT-9, 0.02 % sodium azide-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] DDEF1 SH3-11, 0.5 mM [U-13C; U-15N] APC SAMP1-12, 5 mM sodium phosphate-13, 5 mM [U-2H] DTT-14, 0.02 % sodium phosphate-15, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-15% 13C; U-15N] DDEF1 SH3-16, 0.5 mM [U-15% 13C; U-15N] APC SAMP1-17, 5 mM sodium phosphate-18, 5 mM [U-2H] DTT-19, 0.02 % sodium azide-20, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3AU3 Crystal structure of armadillo repeat domain of APC Deposited 2011-01-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 396–732（337 aa） Fragment：Armadillo repeat, UNP residues 396-732	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；100mM sodium acetate, 1.25M lithium citrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.232
3QHE Crystal structure of the complex between the armadillo repeat domain of adenomatous polyposis coli and the tyrosine-rich domain of Sam68 Deposited 2011-01-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 396–732（337 aa） Fragment：Armadillo repeat domain, residues 396-732	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；100mM BIS-TRIS (pH 5.5), 150mM NaCl, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.230
3QHE Crystal structure of the complex between the armadillo repeat domain of adenomatous polyposis coli and the tyrosine-rich domain of Sam68 Deposited 2011-01-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 396–732（337 aa） Fragment：Armadillo repeat domain, residues 396-732	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；100mM BIS-TRIS (pH 5.5), 150mM NaCl, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.230
3RL7 Crystal structure of hDLG1-PDZ1 complexed with APC Deposited 2011-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K	Resolution 2.30 Å R-free 0.231
3RL7 Crystal structure of hDLG1-PDZ1 complexed with APC Deposited 2011-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K	Resolution 2.30 Å R-free 0.231
3RL7 Crystal structure of hDLG1-PDZ1 complexed with APC Deposited 2011-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K	Resolution 2.30 Å R-free 0.231
3RL7 Crystal structure of hDLG1-PDZ1 complexed with APC Deposited 2011-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K	Resolution 2.30 Å R-free 0.231
3RL7 Crystal structure of hDLG1-PDZ1 complexed with APC Deposited 2011-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K	Resolution 2.30 Å R-free 0.231
3RL7 Crystal structure of hDLG1-PDZ1 complexed with APC Deposited 2011-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K	Resolution 2.30 Å R-free 0.231
3RL8 Crystal structure of hDLG1-PDZ2 complexed with APC Deposited 2011-04-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K	Resolution 2.20 Å R-free 0.245
3T7U A NeW Crystal structure of APC-ARM Deposited 2011-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 407–775（369 aa） Fragment：ARM 1-7 domain, UNP residues 407-775	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；1.02M Sodium phosphate monobasic monohydrate, 0.18M Potassium phosphate dibasic, vapor diffusion, hanging drop, temperature 287K	Resolution 2.90 Å R-free 0.313
3T7U A NeW Crystal structure of APC-ARM Deposited 2011-07-31	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 407–775（369 aa） Fragment：ARM 1-7 domain, UNP residues 407-775	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；1.02M Sodium phosphate monobasic monohydrate, 0.18M Potassium phosphate dibasic, vapor diffusion, hanging drop, temperature 287K	Resolution 2.90 Å R-free 0.313
4G69 Structure of the Human Discs Large 1 PDZ2 - Adenomatous Polyposis Coli Cytoskeletal Polarity Complex Deposited 2012-07-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2833–2843（11 aa） Fragment：APC C-terminal peptide, UNP residues 2833-2843	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；300 K；Protein solution: 1.4 mM Dlg1 PDZ2, 1.7 mM APC, 100 mM NaCl, 25 mM Tris pH 7.0, 0.1% B-ME Well: 200 mM sodium acetate, 100 mM sodium cacodylate pH 6.25, 28% PEG 8000 Drop = 1:1 protein:well solution , VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.00 Å R-free 0.183
4YJE Crystal structure of APC-ARM in complexed with Amer1-A1 Deposited 2015-03-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 407–751（345 aa） Fragment：ARM DOMAIN, UNP RESIDUES 407-751	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；12% PEG 20000	Resolution 1.90 Å R-free 0.221
4YJL Crystal structure of APC-ARM in complexed with Amer1-A2 Deposited 2015-03-03	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 407–751（345 aa） Fragment：ARM DOMAIN, UNP RESIDUES 407-751	Not recorded	EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；287 K；0.2M NACL, 10% PEG 8000	Resolution 2.10 Å R-free 0.225
4YJL Crystal structure of APC-ARM in complexed with Amer1-A2 Deposited 2015-03-03	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 407–751（345 aa） Fragment：ARM DOMAIN, UNP RESIDUES 407-751	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；287 K；0.2M NACL, 10% PEG 8000	Resolution 2.10 Å R-free 0.225
4YJL Crystal structure of APC-ARM in complexed with Amer1-A2 Deposited 2015-03-03	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 C 407–751（345 aa） Fragment：ARM DOMAIN, UNP RESIDUES 407-751	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；287 K；0.2M NACL, 10% PEG 8000	Resolution 2.10 Å R-free 0.225
4YJL Crystal structure of APC-ARM in complexed with Amer1-A2 Deposited 2015-03-03	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 D 407–751（345 aa） Fragment：ARM DOMAIN, UNP RESIDUES 407-751	Not recorded	EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；287 K；0.2M NACL, 10% PEG 8000	Resolution 2.10 Å R-free 0.225
4YJL Crystal structure of APC-ARM in complexed with Amer1-A2 Deposited 2015-03-03	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 E 407–751（345 aa） Fragment：ARM DOMAIN, UNP RESIDUES 407-751	Not recorded	EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；287 K；0.2M NACL, 10% PEG 8000	Resolution 2.10 Å R-free 0.225
4YJL Crystal structure of APC-ARM in complexed with Amer1-A2 Deposited 2015-03-03	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 F 407–751（345 aa） Fragment：ARM DOMAIN, UNP RESIDUES 407-751	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；287 K；0.2M NACL, 10% PEG 8000	Resolution 2.10 Å R-free 0.225
4YK6 Crystal structure of APC-ARM in complexed with Amer1-A4 Deposited 2015-03-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 407–751（345 aa） Fragment：ARM DOMAIN, UNP RESIDUES 407-751	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；287 K；0.2M NACL, 10% PEG8000	Resolution 1.70 Å R-free 0.240
5B6G Protein-protein interaction Deposited 2016-05-27	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 407–751（345 aa） Fragment：UNP RESIDUES 407-751	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2 M Ammonium sulfate, 0.1 M Tris pH 8.0, 25 % w/v PEG 4000	Resolution 1.99 Å R-free 0.215
5IZ6 Protein-protein interaction Deposited 2016-03-25	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 407–751（345 aa） Fragment：UNP RESIDUES 407-751	Not recorded	SO4 SULFATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2M Ammonium sulfate 0.1M Tris pH 8.0, 25% w/v PEG 3350	Resolution 2.15 Å R-free 0.206
5IZ8 Protein-protein interaction Deposited 2016-03-25	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 407–751（345 aa） Fragment：UNP RESIDUES 407-751	Not recorded	PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 4000	Resolution 3.06 Å R-free 0.253
5IZ8 Protein-protein interaction Deposited 2016-03-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 407–751（345 aa） Fragment：UNP RESIDUES 407-751	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 4000	Resolution 3.06 Å R-free 0.253
5IZ9 Protein-protein interaction Deposited 2016-03-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 407–751（345 aa） Fragment：UNP RESIDUES 407-751	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25 % w/v PEG 4000	Resolution 2.93 Å R-free 0.282
5IZA Protein-protein interaction Deposited 2016-03-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 407–751（345 aa） Fragment：UNP RESIDUES 407-751	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 4000	Resolution 1.50 Å R-free 0.159
5Z8H APC with an inhibitor Deposited 2018-01-31	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 407–741（335 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Ammonium sulfate 0.1M Tris pH 8.0, 25% w/v PEG 3350	Resolution 1.79 Å R-free 0.211
7F6M Crystal structure of APC complexed with a peptide inhibitor MAI-516 Deposited 2021-06-25	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 407–751（345 aa）	Not recorded	GOL GLYCEROL × 5 SO4 SULFATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Ammonium sulfate 0.1M Tris pH 8.0, 25% w/v PEG 3350	Resolution 2.40 Å R-free 0.256
7F7O APC-Asef FP assay tracer Deposited 2021-06-30	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 407–738（332 aa）	Not recorded	4CI N-[3',6'-bis(oxidanyl)-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-5-yl]methanethioamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 3350	Resolution 2.80 Å R-free 0.328
7XTY Crystal Structure of the second PDZ domain from human PTPN13 in complex with APC peptide Deposited 2022-05-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；289 K；0.1M citric acid (pH 3.5), 3M NaCl	Resolution 2.10 Å R-free 0.240
7XTY Crystal Structure of the second PDZ domain from human PTPN13 in complex with APC peptide Deposited 2022-05-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2833–2843（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；289 K；0.1M citric acid (pH 3.5), 3M NaCl	Resolution 2.10 Å R-free 0.240
8GSJ APC-Asef tripeptide inhibitor Deposited 2022-09-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 407–738（332 aa）	Not recorded	K8C 2-methylsulfanylpyrimidine-4-carbaldehyde × 1 GLU GLUTAMIC ACID × 1 NAL BETA-(2-NAPHTHYL)-ALANINE × 1 LEU LEUCINE × 1 GJZ (1R,2S)-2-phenylcyclopropanamine × 1 GOL GLYCEROL × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 4000	Resolution 2.10 Å R-free 0.256
8X2Q The Crystal Structure of APC from Biortus. Deposited 2023-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 126–250（125 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；(PEG-G2) 0.2M NaAc pH 7.0, 20% PEG 3350	Resolution 2.00 Å R-free 0.263

27 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 126–250

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1m5i
Deposition date deposition_date	2002-07-09
Structure title title	Crystal Structure of the coiled coil region 129-250 of the tumor suppressor gene product APC
Keywords keywords	coiled-coil, Antitumor protein; ANTITUMOR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.72 Å
Radius of gyration Rg (electron density) rg_electron	22.15 Å
Forward intensity I(0) i0	3369090.00
Molecular weight molecular_weight	12609.0 kDa
Excluded volume excluded_volume	15635 Å³
Envelope volume envelope_volume	19911 Å³
Hydration-shell volume shell_volume	9594 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	24.01 Å
Envelope Rg envelope_rg	22.69 Å
Shape Rg shape_rg	22.13 Å
Total Rg total_rg	22.53 Å
Total atoms total_atoms	883
Residues n_residues	105
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	85.0 Å
Rg (real space) rg_real	22.37 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	3.3690e+06
I(0) uncertainty (real space) i0_real_error	5.2510e+04
Rg (reciprocal space) rg_reciprocal	22.25 Å
I(0) (reciprocal space) i0_reciprocal	3369000.0000
Solution quality estimate total_estimate	0.6770
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	83.7 Å
Skewness Skewness skewness	0.748
Kurtosis Kurtosis kurtosis	-0.032
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	315700.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.287; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.020; Smooth: 0.914

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1m5ia_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.13 — Tumor suppressor gene product Apc
Family Family family	h.4.13.1 — Tumor suppressor gene product Apc

CATH v4.4 (1 domains)

Domain ID domain_id	1m5iA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

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8. Citations (2)

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Unit-cell length a length_a	46.047 Å
Unit-cell length b length_b	46.047 Å
Unit-cell length c length_c	113.299 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2620
R_work r_work	0.2570
R_free r_free	0.3090

Description description	APC protein
Molecular weight formula_weight	14952.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	939

Crystal Structure of the coiled coil region 129-250 of the tumor suppressor gene product APC

1. Protein Identity and Related Structures Protein Identity & Related Structures

APC protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

fit	/app/data/saxs_computation/m5/1m5i/1m5i.fit
pddf	/app/data/pr_computation/m5/1m5i/1m5i.pr.out
profile	/app/data/saxs_computation/m5/1m5i/1m5i.dat