SAXSdb — 4cdg

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

BLOOM SYNDROME 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 636–1298	Fragment：CATALYTIC CORE, RESIDUES 636-1298	NANOBODY × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.1M MES PH 6.0, 22% PEG 20K	Resolution 2.79 Å R-free 0.245
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 636–1298	Fragment：CATALYTIC CORE, RESIDUES 636-1298	NANOBODY × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.1M MES PH 6.0, 22% PEG 20K	Resolution 2.79 Å R-free 0.245

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 4CDG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KV2 Solution Structure of the human BLM HRDC domain Deposited 2010-03-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1210–1294（85 aa） Fragment：HRDC domain, UNP residues 1210-1294	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 1mM [U-99% 13C; U-99% 15N] BLM HRDC domain; 1mM DTT; 20mM HEPES; 100mM sodium chloride; 0.02% sodium azide; 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM [U-99% 13C; U-99% 15N] BLM HRDC domain; 1mM DTT; 20mM HEPES; 100mM sodium chloride; 0.02% sodium azide; 100% D2O \| 100% D2O	Resolution not provided
2MH9 Resonance assignment of RQC domain of human Bloom syndrome protein Deposited 2013-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1067–1210（144 aa） Fragment：UNP RESIDUES 1067-1210	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1 NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] BLM RQC-1, 90 % H2O-2, 10 % D2O-3, 1 mM DTT-4, 20 mM Tris-5, 100 mM Sodium Chloride-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RRD Structure of HRDC domain from human Bloom syndrome protein, BLM Deposited 2010-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1200–1295（96 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；303 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 0.5mM [U-98% 13C; U-98% 15N] BLM-1, 50mM TRIS-2, 100mM sodium chloride-3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM [U-100% 15N] BLM-4, 50mM d11-TRIS-5, 100mM sodium chloride-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM [U-98% 13C; U-98% 15N] BLM-7, 50mM d11-TRIS-8, 100mM sodium chloride-9, 100% D2O \| 100% D2O	Resolution not provided
3WE2 Structure of BLM RQC domain bound to a phosphate ion Deposited 2013-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1068–1209（142 aa） Fragment：RecQ C-terminal (RQC) domain, UNP residues 1068-1209	Not recorded	PO4 PHOSPHATE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.4；293 K；20-25% PEG 4000, 50mM sodium phosphate, 150mM sodium acetate, 100mM Tris-HCl, 15%(v/v) glycerol, pH 8.4, VAPOR DIFFUSION, temperature 293K	Resolution 2.70 Å R-free 0.271
3WE2 Structure of BLM RQC domain bound to a phosphate ion Deposited 2013-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1068–1209（142 aa） Fragment：RecQ C-terminal (RQC) domain, UNP residues 1068-1209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.4；293 K；20-25% PEG 4000, 50mM sodium phosphate, 150mM sodium acetate, 100mM Tris-HCl, 15%(v/v) glycerol, pH 8.4, VAPOR DIFFUSION, temperature 293K	Resolution 2.70 Å R-free 0.271
3WE3 Structure of BLM RQC domain bound to an arsenate ion Deposited 2013-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1068–1209（142 aa） Fragment：RecQ C-terminal (RQC) domain, UNP residues 1068-1209	Not recorded	ART ARSENATE × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.4；293 K；20-25% PEG 4000, 50mM sodium phosphate, 150mM sodium acetate, 100mM Tris-HCl, 15%(v/v) glycerol, pH 8.4, VAPOR DIFFUSION, temperature 293K	Resolution 2.90 Å R-free 0.295
3WE3 Structure of BLM RQC domain bound to an arsenate ion Deposited 2013-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1068–1209（142 aa） Fragment：RecQ C-terminal (RQC) domain, UNP residues 1068-1209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.4；293 K；20-25% PEG 4000, 50mM sodium phosphate, 150mM sodium acetate, 100mM Tris-HCl, 15%(v/v) glycerol, pH 8.4, VAPOR DIFFUSION, temperature 293K	Resolution 2.90 Å R-free 0.295
4CGZ Crystal structure of the Bloom's syndrome helicase BLM in complex with DNA Deposited 2013-11-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 636–1298（663 aa） Fragment：CATALYTIC CORE, RESIDUES 636-1298	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions 21% PEG 4000, 0.1M HEPES PH 7.6, 5% 2-PROPANOL	Resolution 3.20 Å R-free 0.259
4O3M Ternary complex of Bloom's syndrome helicase Deposited 2013-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 640–1298（659 aa）	Not recorded	CA CALCIUM ION × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；6-10% Isopropanol, 50mM MES, 10mM magnesium chloride., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.215
5MK5 Structures of DHBN domain of human BLM helicase Deposited 2016-12-02	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 362–414（53 aa） Fragment：UNP residues 362-414 Chain B 362–414（53 aa） Fragment：UNP residues 362-414	Not recorded	IOD IODIDE ION × 9 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；Tris-HCl 0.1M pH8.5 PEG 1500 26% Glycerol 16%	Resolution 2.16 Å R-free 0.297
5MK5 Structures of DHBN domain of human BLM helicase Deposited 2016-12-02	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 362–414（53 aa） Fragment：UNP residues 362-414 Chain D 362–414（53 aa） Fragment：UNP residues 362-414	Not recorded	IOD IODIDE ION × 11 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；Tris-HCl 0.1M pH8.5 PEG 1500 26% Glycerol 16%	Resolution 2.16 Å R-free 0.297
7AUC Crystal structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM) Deposited 2020-11-02	Different construct 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: monomer	Chain A 636–1070（435 aa） Chain A 1202–1298（97 aa）	Not recorded	ACT ACETATE ION × 4 EDO 1,2-ETHANEDIOL × 6 PG4 TETRAETHYLENE GLYCOL × 2 GOL GLYCEROL × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；Morpheus-HT, condition A8, Molecular Dimensions 0.06 M divalents, 37.5% Buffer System 2 and 37.5% Precipitant Mix 4 Divalents = 0.3M magnesium chloride, 0.3M calcium chloride Buffer system 2 = 1M sodium HEPES, MOPS (acid) pH 7.5 75% Precipitant Mix 4 = 25% w/v MPD, 25% v/v PEG1000, 25% w/v PEG 3350	Resolution 1.53 Å R-free 0.208
7AUD Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM) Deposited 2020-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: protein:DNA complex	Chain F 636–1070（435 aa） Chain F 1202–1298（97 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 RY8 N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；Morpheus HT-96, Condition C9, Molecular Dimensions. 0.09 M NPS, 0.1M Buffer System, 30% Precipitant Mix 1 NPS = 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulphate Buffer System 1 = 1.0 M imidazole, MES monohydrate (acid) pH 6.5 60% Precipitant Mix 1 = 40% v/v PEG 500 MME, 20% w/v PEG 20000	Resolution 2.96 Å R-free 0.269
7AUD Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM) Deposited 2020-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: protein:DNA complex	Chain A 636–1070（435 aa） Chain A 1202–1298（97 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 RY8 N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide × 1 PG4 TETRAETHYLENE GLYCOL × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；Morpheus HT-96, Condition C9, Molecular Dimensions. 0.09 M NPS, 0.1M Buffer System, 30% Precipitant Mix 1 NPS = 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulphate Buffer System 1 = 1.0 M imidazole, MES monohydrate (acid) pH 6.5 60% Precipitant Mix 1 = 40% v/v PEG 500 MME, 20% w/v PEG 20000	Resolution 2.96 Å R-free 0.269
7AUD Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM) Deposited 2020-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: protein:DNA complex	Chain B 636–1070（435 aa） Chain B 1202–1298（97 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 RY8 N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide × 1 PG4 TETRAETHYLENE GLYCOL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；Morpheus HT-96, Condition C9, Molecular Dimensions. 0.09 M NPS, 0.1M Buffer System, 30% Precipitant Mix 1 NPS = 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulphate Buffer System 1 = 1.0 M imidazole, MES monohydrate (acid) pH 6.5 60% Precipitant Mix 1 = 40% v/v PEG 500 MME, 20% w/v PEG 20000	Resolution 2.96 Å R-free 0.269
7AUD Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM) Deposited 2020-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: protein:DNA complex	Chain C 636–1070（435 aa） Chain C 1202–1298（97 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 RY8 N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide × 1 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；Morpheus HT-96, Condition C9, Molecular Dimensions. 0.09 M NPS, 0.1M Buffer System, 30% Precipitant Mix 1 NPS = 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulphate Buffer System 1 = 1.0 M imidazole, MES monohydrate (acid) pH 6.5 60% Precipitant Mix 1 = 40% v/v PEG 500 MME, 20% w/v PEG 20000	Resolution 2.96 Å R-free 0.269
7AUD Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM) Deposited 2020-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–DNA Monomer；Protein × 1 PDB declaration: protein:DNA complex	Chain D 636–1070（435 aa） Chain D 1202–1298（97 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 RY8 N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide × 1 PG4 TETRAETHYLENE GLYCOL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；Morpheus HT-96, Condition C9, Molecular Dimensions. 0.09 M NPS, 0.1M Buffer System, 30% Precipitant Mix 1 NPS = 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulphate Buffer System 1 = 1.0 M imidazole, MES monohydrate (acid) pH 6.5 60% Precipitant Mix 1 = 40% v/v PEG 500 MME, 20% w/v PEG 20000	Resolution 2.96 Å R-free 0.269
7AUD Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM) Deposited 2020-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–DNA Monomer；Protein × 1 PDB declaration: protein:DNA complex	Chain E 636–1070（435 aa） Chain E 1202–1298（97 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 RY8 N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide × 1 PG4 TETRAETHYLENE GLYCOL × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；Morpheus HT-96, Condition C9, Molecular Dimensions. 0.09 M NPS, 0.1M Buffer System, 30% Precipitant Mix 1 NPS = 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulphate Buffer System 1 = 1.0 M imidazole, MES monohydrate (acid) pH 6.5 60% Precipitant Mix 1 = 40% v/v PEG 500 MME, 20% w/v PEG 20000	Resolution 2.96 Å R-free 0.269
7XUW Crystal structure of RPA70N-BLMp2 fusion Deposited 2022-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–570（21 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；278 K；8% PEG 4000	Resolution 1.80 Å R-free 0.217
7XV0 Crystal structure of RPA70N-BLMp1 fusion Deposited 2022-05-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 146–165（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；278 K；2000 mM Ammonium sulfate	Resolution 1.50 Å R-free 0.200

12 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BLM_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–665； UniProt 636–1298 Author chain B； PDBConstruct 3–665； UniProt 636–1298

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	4cdg
Deposition date deposition_date	2013-10-31
Structure title title	Crystal structure of the Bloom's syndrome helicase BLM in complex with Nanobody
Keywords keywords	HYDROLASE; HYDROLASE
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	42.14 Å
Radius of gyration Rg (electron density) rg_electron	41.57 Å
Forward intensity I(0) i0	420155000.00
Molecular weight molecular_weight	166870.0 kDa
Excluded volume excluded_volume	208290 Å³
Envelope volume envelope_volume	304650 Å³
Hydration-shell volume shell_volume	60047 Å³
Envelope diameter envelope_diameter	129.8 Å
Shell Rg shell_rg	48.60 Å
Envelope Rg envelope_rg	40.13 Å
Shape Rg shape_rg	41.58 Å
Total Rg total_rg	41.87 Å
Total atoms total_atoms	11711
Residues n_residues	1485
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	126.4 Å
Rg (real space) rg_real	41.98 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	4.2020e+08
I(0) uncertainty (real space) i0_real_error	6.6500e+06
Rg (reciprocal space) rg_reciprocal	42.14 Å
I(0) (reciprocal space) i0_reciprocal	420200000.0000
Solution quality estimate total_estimate	0.8864
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	64.9 Å
Skewness Skewness skewness	0.050
Kurtosis Kurtosis kurtosis	-0.744
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	59540000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.598

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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	BLOOM SYNDROME PROTEIN
Molecular weight formula_weight	76705.2 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11711

SMSRNLKHERFQSLSFPHTKEMMKIFHKKFGLHNFRTNQLEAINAALLGEDCFILMPTGGGKSLCYQLPACVSPGVTVVISPLRSLIVDQVQKLTSLDIPATYLTGDKTDSEATNIYLQLSKKDPIIKLLYVTPEKICASNRLISTLENLYERKLLARFVIDEAHCVSQWGHDFRQDYKRMNMLRQKFPSVPVMALTATANPRVQKDILTQLKILRPQVFSMSFNRHNLKYYVLPKKPKKVAFDCLEWIRKHHPYDSGIIYCLSRRECDTMADTLQRDGLAALAYHAGLSDSARDEVQQKWINQDGCQVICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEISHCLLFYTYHDVTRLKRLIMMEKDGNHHTRETHFNNLYSMVHYCENITECRRIQLLAYFGENGFNPDFCKKHPDVSCDNCCKTKDYKTRDVTDDVKSIVRFVQEHSSSQGMRNIKHVGPSGRFTMNMLVDIFLGSKSAKIQSGIFGKGSAYSRHNAERLFKKLILDKILDEDLYINANDQAIAYVMLGNKAQTVLNGNLKVDFMETENSSSVKKQKALVAKVSQREEMVKKCLGELTEVCKSLGKVFGVHYFNIFNTVTLKKLAESLSSDPEVLLQIDGVTEDKLEKYGAEVISVLQKYSEWTSPAEDSSPGMSENLYFQ

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

Entity 2 Entity 2 polymer

Description description	NANOBODY
Molecular weight formula_weight	16170.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQAGGSLRLSCAASGIWFSINNMAWYRQTPGKQRERIAIITSAGTTNYVDSVKGRFTISRDDAKNTMYLQMNSLIPEDTAVYYCNLVADYDMGFQSFWGRGTQVTVSSHHHHHH

来源 Source

来源生物 organism	LAMA GLAMA
通用名 common_name	LLAMA
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4cdgc1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4cdgc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4cdgd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4cdgd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (10 domains)

Domain ID domain_id	4cdgA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4cdgA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4cdgA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	4cdgA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

Domain ID domain_id	4cdgB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4cdgB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4cdgB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	4cdgB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

Domain ID domain_id	4cdgC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4cdgD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	59.666 Å
Unit-cell length b length_b	88.425 Å
Unit-cell length c length_c	95.120 Å
Unit-cell angle α angle_alpha	69.39 °
Unit-cell angle β angle_beta	89.84 °
Unit-cell angle γ angle_gamma	77.07 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.794 Å
Low-resolution limit resolution_low	42.881 Å
R factor r_factor	0.2076
R_work r_work	0.2056
R_free r_free	0.2455

fit	/app/data/saxs_computation/cd/4cdg/4cdg.fit
pddf	/app/data/pr_computation/cd/4cdg/4cdg.pr.out
profile	/app/data/saxs_computation/cd/4cdg/4cdg.dat

Crystal structure of the Bloom's syndrome helicase BLM in complex with Nanobody

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

BLOOM SYNDROME 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 non-polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)