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4qpm

Structure of Bub1 kinase domain

Method: X-RAY DIFFRACTION Dmax: 101.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mitotic checkpoint serine/threonine-protein kinase BUB1

Homo sapiens

UniProt O43683

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 749–1094 Fragment：UNP residues 749-1094 Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；293 K；20% PEG3350, 1% Tryptone, 10 mM DTT, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.269
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 749–1094 Fragment：UNP residues 749-1094 Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；293 K；20% PEG3350, 1% Tryptone, 10 mM DTT, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.269

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 4QPM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LAH Solution NMR Structure of Mitotic checkpoint serine/threonine-protein kinase BUB1 N-terminal domain from Homo sapiens, Northeast Structural Genomics Consortium Target HR5460A (Methods Development) Deposited 2011-03-14 Different construct Different mutation/modification 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 1–150（150 aa） Fragment：N-terminal domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Pressure ambient
NMR sample composition 1.164 mM [U-100% 13C; U-100% 15N] HR5460A, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.033 mM [U-10% 13C; U-100% 15N] HR5460A, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
4A1G The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1 Deposited 2011-09-15 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 1–150（150 aa） Fragment：TPR DOMAIN, RESIDUES 1-150
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.25-1.3 M NA MALONATE, PH 6.0.
Resolution 2.60 Å R-free 0.244
4A1G The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1 Deposited 2011-09-15 Different construct Different mutation/modification 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 1–150（150 aa） Fragment：TPR DOMAIN, RESIDUES 1-150
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.25-1.3 M NA MALONATE, PH 6.0.
Resolution 2.60 Å R-free 0.244
4A1G The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1 Deposited 2011-09-15 Different construct Different mutation/modification 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 1–150（150 aa） Fragment：TPR DOMAIN, RESIDUES 1-150
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.25-1.3 M NA MALONATE, PH 6.0.
Resolution 2.60 Å R-free 0.244
4A1G The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1 Deposited 2011-09-15 Different construct Different mutation/modification 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 1–150（150 aa） Fragment：TPR DOMAIN, RESIDUES 1-150
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；1.25-1.3 M NA MALONATE, PH 6.0.
Resolution 2.60 Å R-free 0.244
4R8Q Structure and substrate recruitment of the human spindle checkpoint kinase bub1 Deposited 2014-09-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 724–1085（362 aa） Fragment：Kinase domain, unp residues 724-1085
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.29；293 K；TO 15 MG/ML BUB1, ATP WAS ADDED TO A FINAL CONCENTRATION OF 10 MM. SITTING DROPS WERE MADE BY MIXING 1.5 MICROLITERS PROTEIN WITH 1.5 MICROLITERS CRYSTALLIZATION SOLUTION (20% W/V PEG 3350, 0.1 M SODIUM FORMATE PH 6.29, 25 MM DTT) AND EQUILIBRATING AGAINST 200 MICROLITERS OF RESERVOIR SOLUTION. LARGE SINGLE CRYSTALS WERE OBTAINED BY REPEATED SEEDING. THE CRYSTALS WERE CRYO-PROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 18% V/V GLYCEROL AND THEN FLASH-COOLED IN LIQUID PROPANE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, vapor diffusion, sitting drop
Resolution 2.31 Å R-free 0.264
5DMZ Structure of human Bub1 kinase domain phosphorylated at Ser969 Deposited 2015-09-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 726–1085（360 aa） Fragment：UNP residues 726-1085
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；277 K；0.2 M NaCl, 15% PEG 3350
Resolution 2.40 Å R-free 0.245
5DMZ Structure of human Bub1 kinase domain phosphorylated at Ser969 Deposited 2015-09-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 726–1085（360 aa） Fragment：UNP residues 726-1085
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；277 K；0.2 M NaCl, 15% PEG 3350
Resolution 2.40 Å R-free 0.245
6F7B Crystal structure of the human Bub1 kinase domain in complex with BAY 1816032 Deposited 2017-12-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 726–1085（360 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CVQ 2-[3,5-bis(fluoranyl)-4-[[3-[5-methoxy-4-[(3-methoxypyridin-4-yl)amino]pyrimidin-2-yl]indazol-1-yl]methyl]phenoxy]ethanol × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.26；277 K；200mM MgCl2, 100mM Tris-HCl pH 7.26, 5% glycerol, 20% PEG 3350
Resolution 2.00 Å R-free 0.254
7B1F Orthorhombic P212121 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain Deposited 2020-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 455–479（25 aa）
Chain D 455–479（25 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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；293 K；20% PEG 4000, 0.1 M Hepes pH 7.5, 10% isopropanol
Resolution 1.75 Å R-free 0.287
7B1H Monoclinic P21 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain Deposited 2020-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 455–479（25 aa）
Chain D 455–479（25 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 7.5；293 K；8% Isopropanol, 20% PEG 4000, 0.1 M Na HEPES, pH 7.5
Resolution 2.40 Å R-free 0.281
7B1H Monoclinic P21 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain Deposited 2020-11-24 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 G 455–479（25 aa）
Chain H 455–479（25 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 7.5；293 K；8% Isopropanol, 20% PEG 4000, 0.1 M Na HEPES, pH 7.5
Resolution 2.40 Å R-free 0.281
7B1J Orthorhombic P21212 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain Deposited 2020-11-25 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 C 455–479（25 aa）
Chain D 455–479（25 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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；293 K；10% Isopropanol, 0.1 M Na HEPES, pH 7.5, 20% PEG 4000
Resolution 2.90 Å R-free 0.296

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BUB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 11–356； UniProt 749–1094 Author chain B； PDBConstruct 11–356； UniProt 749–1094

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

SAXS profile for 4qpm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qpm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4qpm
Deposition date deposition_date2014-06-24
Structure title titleStructure of Bub1 kinase domain
Keywords keywordsTransferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.59 Å
Radius of gyration Rg (electron density) rg_electron29.91 Å
Forward intensity I(0) i089122900.00
Molecular weight molecular_weight77239.0 kDa
Excluded volume excluded_volume97781 ų
Envelope volume envelope_volume122460 ų
Hydration-shell volume shell_volume34524 ų
Envelope diameter envelope_diameter99.6 Å
Shell Rg shell_rg36.49 Å
Envelope Rg envelope_rg29.81 Å
Shape Rg shape_rg29.91 Å
Total Rg total_rg30.54 Å
Total atoms total_atoms10807
Residues n_residues657
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax101.0 Å
Rg (real space) rg_real30.65 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real8.9120e+07
I(0) uncertainty (real space) i0_real_error1.4260e+06
Rg (reciprocal space) rg_reciprocal30.63 Å
I(0) (reciprocal space) i0_reciprocal89120000.0000
Solution quality estimate total_estimate0.8844
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.1 Å
Skewness Skewness skewness0.377
Kurtosis Kurtosis kurtosis-0.465
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44580000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.925
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4qpmA01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id4qpmA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4qpmB01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily20 —
Domain ID domain_id4qpmB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)