SAXSdb — 6f7b

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

Mitotic checkpoint serine/threonine-protein kinase BUB1

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 726–1085	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

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 6F7B	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
4QPM Structure of Bub1 kinase domain Deposited 2014-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 749–1094（346 aa） 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
4QPM Structure of Bub1 kinase domain Deposited 2014-06-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 749–1094（346 aa） 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
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
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 14 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 2–361； UniProt 726–1085

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	6f7b
Deposition date deposition_date	2017-12-08
Structure title title	Crystal structure of the human Bub1 kinase domain in complex with BAY 1816032
Keywords keywords	BUB1, kinase inhibitor, transferase; TRANSFERASE
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	21.65 Å
Radius of gyration Rg (electron density) rg_electron	20.59 Å
Forward intensity I(0) i0	25464100.00
Molecular weight molecular_weight	40221.0 kDa
Excluded volume excluded_volume	51031 Å³
Envelope volume envelope_volume	60013 Å³
Hydration-shell volume shell_volume	23788 Å³
Envelope diameter envelope_diameter	70.6 Å
Shell Rg shell_rg	27.66 Å
Envelope Rg envelope_rg	20.99 Å
Shape Rg shape_rg	20.60 Å
Total Rg total_rg	21.53 Å
Total atoms total_atoms	2829
Residues n_residues	342
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	69.2 Å
Rg (real space) rg_real	21.54 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.5460e+07
I(0) uncertainty (real space) i0_real_error	3.3180e+05
Rg (reciprocal space) rg_reciprocal	21.56 Å
I(0) (reciprocal space) i0_reciprocal	25460000.0000
Solution quality estimate total_estimate	0.7108
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.226
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8359000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 0.207; Positv: 1.000; Valcen: 1.000; Smooth: 0.982

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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 checkpoint serine/threonine-protein kinase BUB1
Molecular weight formula_weight	41484.0 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3055

GSSLGTVDAPNFIVGNPWDDKLIFKLLSGLSKPVSSYPNTFEWQCKLPAIKPKTEFQLGSKLVYVHHLLGEGAFAQVYEATQGDLNDAKNKQKFVLKVQKPANPWEFYIGTQLMERLKPSMQHMFMKFYSAHLFQNGSVLVGELYSYGTLLNAINLYKNTPEKVMPQGLVISFAMRMLYMIEQVHDCEIIHGDIKPDNFILGNGFLEQDDEDDLSAGLALIDLGQSIDMKLFPKGTIFTAKCETSGFQCVEMLSNKPWNYQIDYFGVAATVYCMLFGTYMKVKNEGGECKPEGLFRRLPHLDMWNEFFHVMLNIPDCHHLPSLDLLRQKLKKVFQQHYTNKIRALRNRLIVLLLECKRSRK

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	Trichoplusia ni

Entity 2 Entity 2 non-polymer

Description description	2-[3,5-bis(fluoranyl)-4-[[3-[5-methoxy-4-[(3-methoxypyridin-4-yl)amino]pyrimidin-2-yl]indazol-1-yl]methyl]phenoxy]ethanol
Molecular weight formula_weight	534.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6f7bA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	130 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6f7bA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	50.497 Å
Unit-cell length b length_b	60.093 Å
Unit-cell length c length_c	124.469 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	4

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	46.790 Å
R factor r_factor	0.2010
R_work r_work	0.1983
R_free r_free	0.2537

fit	/app/data/saxs_computation/f7/6f7b/6f7b.fit
pddf	/app/data/pr_computation/f7/6f7b/6f7b.pr.out
profile	/app/data/saxs_computation/f7/6f7b/6f7b.dat

Crystal structure of the human Bub1 kinase domain in complex with BAY 1816032

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

Mitotic checkpoint serine/threonine-protein kinase BUB1

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