SAXSdb — 2qyf

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

Mitotic spindle assembly checkpoint protein MAD2A

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–205	Mutation：L13A Non-standard monomer：Yes (specific site not provided by mmCIF)	MAD2L1-binding protein × 1 （Q15013） peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；16% (w/v) PEG 3350, 16% (v/v) glycerol, 125 mM sodium phosphate (pH 5.0), 100 mM NaCl, 25 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.257
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–205	Mutation：L13A Non-standard monomer：Yes (specific site not provided by mmCIF)	MAD2L1-binding protein × 1 （Q15013） peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；16% (w/v) PEG 3350, 16% (v/v) glycerol, 125 mM sodium phosphate (pH 5.0), 100 mM NaCl, 25 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.257

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 2QYF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DUJ SOLUTION STRUCTURE OF THE SPINDLE ASSEMBLY CHECKPOINT PROTEIN HUMAN MAD2 Deposited 2000-01-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–195（185 aa） Fragment：FULL PROTEIN WITHOUT BOTH N- AND C-TERMINAL 10 RESIDUES	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 300mM KCl；Pressure ambient NMR sample composition 1.2mM Mad2 protein U-15N,13C,2H; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.4mM Mad2 protein U-15N,13C; U-60% 2H; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.5mM Mad2 protein U-15N; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.6mM Mad2 protein U-10% 13C; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 100% D2O \| 100% D2O NMR sample composition 1.7mM Mad2 protein U-15N,13C; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 100% D2O \| 100% D2O	Resolution not provided
1GO4 Crystal structure of Mad1-Mad2 reveals a conserved Mad2 binding motif in Mad1 and Cdc20. Deposited 2001-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–205（205 aa） Chain B 1–205（205 aa） Chain C 1–205（205 aa） Chain D 1–205（205 aa）	Mutation：R133A Mutation：R133A Mutation：R133A Mutation：R133A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；PROTEIN CONCENTRATION 7.5 MG/ML HANGING DROP METHOD, WELL=100 MM AMMONIUM SULPHATE, 100 MM AMMONIUM CITRATE PH 5.2, 10 MM DTT	Resolution 2.05 Å R-free 0.268
1KLQ The Mad2 Spindle Checkpoint Protein Undergoes Similar Major Conformational Changes upon Binding to Either Mad1 or Cdc20 Deposited 2001-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 9–205（197 aa） Fragment：MISSING N-TERMINAL 10 RESIDUES	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR sample composition 0.8mM Mad2 protein U-15N; 1mM MBP1 NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM Mad2 protein U-15N, 13C, 2H; 1mM MBP1 NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM Mad2 protein U-15N, 13C; 1mM MBP1 NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM Mad2 protein U-15N, 13C, U-60% 2H; 1mM MBP1 NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM MBP1 U-15N; 1mM Mad2 protein NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8mM MBP1 U-15N, 13C; 1mM Mad2 protein NA; 50mM phosphate buffer; 0.3M KCl; 1mM DTT \| 90% H2O/10% D2O	Resolution not provided
1S2H The Mad2 spindle checkpoint protein possesses two distinct natively folded states Deposited 2004-01-08	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–205（205 aa）	Mutation：R133A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.3M KCl；Pressure ambient NMR sample composition 0.8mM Mad2 protein U-15N,13C,2H \| 90% H2O, 10% D2O; 50mM phosphate buffer; 0.3M KCl; 1mM DTT NMR sample composition 0.8mM Mad2 protein U-15N \| 90% H2O, 10% D2O; 50mM phosphate buffer; 0.3M KCl; 1mM DTT NMR sample composition 0.8mM Mad2 protein U-15N,13C \| 90% H2O, 10% D2O; 50mM phosphate buffer; 0.3M KCl; 1mM DTT	Resolution not provided
2V64 Crystallographic structure of the conformational dimer of the Spindle Assembly Checkpoint protein Mad2. Deposited 2007-07-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–205（204 aa） Fragment：RESIDUES 2-205 Chain E 2–108（107 aa） Fragment：RESIDUES 2-108,118-205 Chain E 118–205（88 aa） Fragment：RESIDUES 2-108,118-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M NAACETATE PH 4.6, 3.5M NAFORMATE	Resolution 2.90 Å R-free 0.273
2V64 Crystallographic structure of the conformational dimer of the Spindle Assembly Checkpoint protein Mad2. Deposited 2007-07-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–205（204 aa） Fragment：RESIDUES 2-205 Chain D 2–108（107 aa） Fragment：RESIDUES 2-108,118-205 Chain D 118–205（88 aa） Fragment：RESIDUES 2-108,118-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M NAACETATE PH 4.6, 3.5M NAFORMATE	Resolution 2.90 Å R-free 0.273
2V64 Crystallographic structure of the conformational dimer of the Spindle Assembly Checkpoint protein Mad2. Deposited 2007-07-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 2–205（204 aa） Fragment：RESIDUES 2-205 Chain H 2–108（107 aa） Fragment：RESIDUES 2-108,118-205 Chain H 118–205（88 aa） Fragment：RESIDUES 2-108,118-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M NAACETATE PH 4.6, 3.5M NAFORMATE	Resolution 2.90 Å R-free 0.273
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification 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 1–205（205 aa）	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 1–205（205 aa）	Mutation：YES	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain K 1–205（205 aa）	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 1–205（205 aa）	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification 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 1–205（205 aa）	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 4 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification 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 1–205（205 aa）	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification 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 1–205（205 aa）	Mutation：YES	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–205（205 aa）	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 5 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–205（205 aa）	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–205（205 aa）	Mutation：YES	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1–205（205 aa）	Mutation：YES	PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
2VFX Structure of the Symmetric Mad2 Dimer Deposited 2007-11-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 1–205（205 aa）	Mutation：YES	CL CHLORIDE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2	Resolution 1.95 Å R-free 0.247
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 11–205（195 aa） Chain B 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 11–205（195 aa） Chain D 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 11–205（195 aa） Chain F 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	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 G 11–205（195 aa） Chain H 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 11–205（195 aa） Chain J 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
3GMH Crystal Structure of the Mad2 Dimer Deposited 2009-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 11–205（195 aa） Chain L 11–205（195 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；1.6M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.95 Å R-free 0.251
5KHU Model of human Anaphase-promoting complex/Cyclosome (APC15 deletion mutant), in complex with the Mitotic checkpoint complex (APC/C-CDC20-MCC) based on cryo EM data at 4.8 Angstrom resolution Deposited 2016-06-15	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain T 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
5LCW Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 4.2 angstrom resolution Deposited 2016-06-22	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain Z 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6F0X Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20 Deposited 2017-11-20	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 × 9 PDB declaration: nonameric	Chain Z 1–205（205 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6TLJ Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 3.8 angstrom resolution Deposited 2019-12-02	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain Z 1–205（205 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å

11 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MD2L1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–206； UniProt 1–205 Author chain C； PDBConstruct 2–206； UniProt 1–205

MAD2L1-binding protein

Homo sapiens

UniProt Q15013

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 36–274	Fragment：UNP residues 36-274 Non-standard monomer：Yes (specific site not provided by mmCIF)	Mitotic spindle assembly checkpoint protein MAD2A × 1 （Q13257） peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；16% (w/v) PEG 3350, 16% (v/v) glycerol, 125 mM sodium phosphate (pH 5.0), 100 mM NaCl, 25 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.257
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 36–274	Fragment：UNP residues 36-274 Non-standard monomer：Yes (specific site not provided by mmCIF)	Mitotic spindle assembly checkpoint protein MAD2A × 1 （Q13257） peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；16% (w/v) PEG 3350, 16% (v/v) glycerol, 125 mM sodium phosphate (pH 5.0), 100 mM NaCl, 25 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.257

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 2QYF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6F0X Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20 Deposited 2017-11-20	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 × 9 PDB declaration: nonameric	Chain P 1–274（274 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MD2BP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–240； UniProt 36–274 Author chain D； PDBConstruct 2–240； UniProt 36–274

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2qyf
Deposition date deposition_date	2007-08-14
Structure title title	Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex
Keywords keywords	PROTEIN-PEPTIDE COMPLEX, MAD2 FAMILY, SPINDLE ASSEMBLY CHECKPOINT, Cell cycle, Cell division, Mitosis, Nucleus, Phosphorylation; CELL CYCLE
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	30.73 Å
Radius of gyration Rg (electron density) rg_electron	29.64 Å
Forward intensity I(0) i0	123580000.00
Molecular weight molecular_weight	89814.0 kDa
Excluded volume excluded_volume	113130 Å³
Envelope volume envelope_volume	141620 Å³
Hydration-shell volume shell_volume	39148 Å³
Envelope diameter envelope_diameter	97.6 Å
Shell Rg shell_rg	37.35 Å
Envelope Rg envelope_rg	29.67 Å
Shape Rg shape_rg	29.65 Å
Total Rg total_rg	30.37 Å
Total atoms total_atoms	6286
Residues n_residues	768
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	92.2 Å
Rg (real space) rg_real	30.60 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.2360e+08
I(0) uncertainty (real space) i0_real_error	1.7750e+06
Rg (reciprocal space) rg_reciprocal	30.66 Å
I(0) (reciprocal space) i0_reciprocal	123600000.0000
Solution quality estimate total_estimate	0.9128
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.5 Å
Skewness Skewness skewness	0.159
Kurtosis Kurtosis kurtosis	-0.626
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30920000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Mitotic spindle assembly checkpoint protein MAD2A
Molecular weight formula_weight	23595.8 kDa
Mutation mutation	L13A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6944

GMALQLSREQGITARGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND

来源 Source

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(DE3)

Entity 2 Entity 2 polymer

Description description	MAD2L1-binding protein
Molecular weight formula_weight	27687.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MTSSTQEPLNASEAFCPRDCMVPVVFPGPVSQEGCCQFTCELLKHIMYQRQQLPLPYEQLKHFYRKPSPQAEEMLKKKPRATTEVSSRKCQQALAELESVLSHLEDFFARTLVPRVLILLGGNALSPKEFYELDLSLLAPYSVDQSLSTAACLRRLFRAIFMADAFSELQAPPLMGTVVMAQGHRNCGEDWFRPKLNYRVPSRGHKLTVTLSCGRPSIRTTAWEDYIWFQAPVTFKGFRE

来源 Source

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(DE3)

Entity 3 Entity 3 polymer

Description description	peptide
Molecular weight formula_weight	1451.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

SWYSYPPPQRAV

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	658

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2qyfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2qyfc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

CATH v4.4 (4 domains)

Domain ID domain_id	2qyfA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2qyfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2qyfC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2qyfD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	20 —

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8. Citations (4)

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Unit-cell length a length_a	68.667 Å
Unit-cell length b length_b	104.519 Å
Unit-cell length c length_c	138.825 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1898
R_work r_work	0.1870
R_free r_free	0.2567

fit	/app/data/saxs_computation/qy/2qyf/2qyf.fit
pddf	/app/data/pr_computation/qy/2qyf/2qyf.pr.out
profile	/app/data/saxs_computation/qy/2qyf/2qyf.dat

Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex

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

Mitotic spindle assembly checkpoint protein MAD2A

State in the Current Structure

Other States of the Same Protein in the Database

MAD2L1-binding 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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)