SAXSdb — 6b5q

▼

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

DCN1-like protein 1

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 58–259	Not recorded	Peptidomimetic Inhibitors DI-591 × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；37 % PEG 300, 0.1 M phosphate-citrate pH 4.2	Resolution 2.16 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 58–259	Not recorded	Peptidomimetic Inhibitors DI-591 × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；37 % PEG 300, 0.1 M phosphate-citrate pH 4.2	Resolution 2.16 Å R-free 0.241

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 6B5Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TDU N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex Deposited 2011-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 62–259（198 aa） Fragment：unp residues 62-259	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；276 K；27% PEG1500, 0.1M MIB, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 276K	Resolution 1.50 Å R-free 0.232
3TDU N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex Deposited 2011-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 62–259（198 aa） Fragment：unp residues 62-259	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；276 K；27% PEG1500, 0.1M MIB, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 276K	Resolution 1.50 Å R-free 0.232
3TDZ N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-stapled acetylated Ubc12N complex Deposited 2011-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 62–259（198 aa） Fragment：unp residues 62-259	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21% PEG3350, 0.2M KCl, pH Unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.224
3TDZ N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-stapled acetylated Ubc12N complex Deposited 2011-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 62–259（198 aa） Fragment：unp residues 62-259	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21% PEG3350, 0.2M KCl, pH Unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.224
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 62–259（198 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP	Resolution 3.11 Å R-free 0.284
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 62–259（198 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP	Resolution 3.11 Å R-free 0.284
5UFI DCN1 bound to DI-591 Deposited 2017-01-04	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 58–259（202 aa） Fragment：UNP residues 58-259	Not recorded	8B1 N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 4000 and 100 mM potassium phosphate (monobasic)	Resolution 2.58 Å R-free 0.240
5UFI DCN1 bound to DI-591 Deposited 2017-01-04	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 58–259（202 aa） Fragment：UNP residues 58-259	Not recorded	8B1 N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 4000 and 100 mM potassium phosphate (monobasic)	Resolution 2.58 Å R-free 0.240
5UFI DCN1 bound to DI-591 Deposited 2017-01-04	Different construct 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 58–259（202 aa） Fragment：UNP residues 58-259	Not recorded	8B1 N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 4000 and 100 mM potassium phosphate (monobasic)	Resolution 2.58 Å R-free 0.240
5UFI DCN1 bound to DI-591 Deposited 2017-01-04	Different construct 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 58–259（202 aa） Fragment：UNP residues 58-259	Not recorded	8B1 N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 4000 and 100 mM potassium phosphate (monobasic)	Resolution 2.58 Å R-free 0.240
5V83 Structure of DCN1 bound to NAcM-HIT Deposited 2017-03-21	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 62–259（198 aa）	Not recorded	8Z7 N-(1-benzylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；6% PEG3350, 0.2M NH4Br	Resolution 2.00 Å R-free 0.229
5V86 Structure of DCN1 bound to NAcM-OPT Deposited 2017-03-21	Different construct Different mutation/modification 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 62–259（198 aa） Fragment：residues 62-259	Mutation：D127A, R154A	8ZA N-benzyl-N-(1-butylpiperidin-4-yl)-N'-(3,4-dichlorophenyl)urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；6% PEG3350, 0.2M NH4Br	Resolution 1.37 Å R-free 0.195
5V88 Structure of DCN1 bound to NAcM-COV Deposited 2017-03-21	Different construct Different mutation/modification 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 62–259（198 aa）	Mutation：D127A, R154A	8ZD N-{2-[({1-[(2R)-pentan-2-yl]piperidin-4-yl}{[3-(trifluoromethyl)phenyl]carbamoyl}amino)methyl]phenyl}propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；6% PEG3350, 0.2M NH4Br	Resolution 1.60 Å R-free 0.189
6BG3 Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl acetate bound to DCN1 Deposited 2017-10-27	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 62–259（198 aa） Fragment：PONY	Not recorded	DOJ N-{(3S,4S)-1-benzyl-3-[(1S)-1-hydroxyethoxy]piperidin-4-yl}-N'-[3-(trifluoromethyl)phenyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；277 K；6% PEG3350, 0.2M NH4Br	Resolution 1.05 Å R-free 0.173
6BG5 Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluoromethyl)phenyl)urea bound to DCN1 Deposited 2017-10-27	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 62–259（198 aa） Fragment：PONY	Not recorded	DQD N-[(2H-1,3-benzodioxol-5-yl)methyl]-N-(1-propylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；277 K；6% PEG3350, 0.2M NH4Br	Resolution 1.10 Å R-free 0.172
6P5V Structure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)-3-methylbenzamide Deposited 2019-05-31	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 62–259（198 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 O37 N-[(4S,5S)-1-[(1S)-cyclohex-3-en-1-yl]-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-3-methylbenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；7% PEG3350, 0.2M NH4Br	Resolution 1.40 Å R-free 0.205
6P5W Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)benzamide Deposited 2019-05-31	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 62–259（198 aa）	Not recorded	O0A 3-methyl-N-[(4S,5S)-3-methyl-4-(4-methylphenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；6% PEG3350, 0.2M NH4Br	Resolution 1.69 Å R-free 0.222
6XOL DCN1 bound to DI-1548 Deposited 2020-07-07	Different construct Different mutation/modification 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 62–259（198 aa）	Mutation：C54T,C97A,D127A,A146T,R154A	H8S N-{(1S)-1-cyclohexyl-2-[(2-methylpropanoyl)amino]ethyl}-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；28-33 % PEG3350, 200 mM ammonium formate	Resolution 2.39 Å R-free 0.264
6XOM DCN1 bound to 8 Deposited 2020-07-07	Different construct Different mutation/modification 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 62–259（198 aa）	Mutation：C54T,C97A,D127A,A146T,R154A	EDO 1,2-ETHANEDIOL × 1 H8V (2R)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alanyl}amino)ethyl]-2-methyl-4-(morpholin-4-yl)butanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；28 - 33% PEG 3350, 200 mM ammonium formate	Resolution 2.10 Å R-free 0.243
6XON DCN1 bound to inhibitor 9 Deposited 2020-07-07	Different construct Different mutation/modification 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 62–259（198 aa）	Mutation：C54T,C97A,D127A,A146T,R154A	H9M (2S)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alanyl}amino)ethyl]-4-(dimethylamino)-2-methylbutanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；28-33% PEG 3350, 0.2 M ammonium formate	Resolution 2.80 Å R-free 0.289
6XOO DCN1 bound to DI-1859 Deposited 2020-07-07	Different construct Different mutation/modification 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 62–259（198 aa）	Mutation：C54T,C97A,D127A,A146T,R154A	H8S N-{(1S)-1-cyclohexyl-2-[(2-methylpropanoyl)amino]ethyl}-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；28-33% PEG 3350, 200 mM Ammonium formate	Resolution 2.06 Å R-free 0.242
6XOP DCN1 bound to inhibitor 10 Deposited 2020-07-07	Different construct Different mutation/modification 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 62–259（198 aa）	Mutation：C54T,C97A,D127A,A146T,R154A	H9P N-[(1S)-1-cyclohexyl-2-{[(2S)-3-(1H-imidazol-1-yl)-2-methylpropanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；28-33% PEG 3350, 0.2 M ammonium formate	Resolution 2.07 Å R-free 0.247
6XOQ DCN1 covalently bound to inhibitor 4 Deposited 2020-07-07	Different construct Different mutation/modification 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 62–259（198 aa）	Mutation：C54T,C97A,D127A,A146T,R154A	H9S (2E)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alanyl}amino)ethyl]-4-(morpholin-4-yl)but-2-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；28-33% PEG 3350, 0.2 M ammonium formate	Resolution 2.07 Å R-free 0.247
7KWA Structure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)-3-(trifluoromethyl)benzamide Deposited 2020-11-30	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 62–259（198 aa）	Not recorded	YHP N-[(4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-3-(trifluoromethyl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；277 K；6% PEG3350, 0.2M NH4Br	Resolution 1.57 Å R-free 0.209
8OR2 CAND1-CUL1-RBX1-DCNL1 Deposited 2023-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–259（259 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8OR3 CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1 Deposited 2023-04-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–259（259 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

20 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DCNL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–225； UniProt 58–259 Author chain B； PDBConstruct 24–225； UniProt 58–259

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6b5q
Deposition date deposition_date	2017-09-29
Structure title title	DCN1 bound to 38
Keywords keywords	E3 ligase, complex, Ligase-Inhibitor complex, LIGASE; Ligase/Inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	23.09 Å
Radius of gyration Rg (electron density) rg_electron	22.01 Å
Forward intensity I(0) i0	30771700.00
Molecular weight molecular_weight	44432.0 kDa
Excluded volume excluded_volume	56298 Å³
Envelope volume envelope_volume	65829 Å³
Hydration-shell volume shell_volume	25014 Å³
Envelope diameter envelope_diameter	78.8 Å
Shell Rg shell_rg	28.88 Å
Envelope Rg envelope_rg	22.12 Å
Shape Rg shape_rg	22.00 Å
Total Rg total_rg	22.90 Å
Total atoms total_atoms	3226
Residues n_residues	376
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

▼

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

Maximum dimension Dmax dmax	78.3 Å
Rg (real space) rg_real	23.02 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	3.0770e+07
I(0) uncertainty (real space) i0_real_error	4.7550e+05
Rg (reciprocal space) rg_reciprocal	23.04 Å
I(0) (reciprocal space) i0_reciprocal	30770000.0000
Solution quality estimate total_estimate	0.8762
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.287
Kurtosis Kurtosis kurtosis	-0.289
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13690000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DCN1-like protein 1
Molecular weight formula_weight	26251.9 kDa
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	3341

MSYYHHHHHHLESTSLYKKAGTMGSLDRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV

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	Peptidomimetic Inhibitors DI-591
Molecular weight formula_weight	725.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

XXXKX

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6b5qA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	6b5qB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

▶

8. Citations (1)

▶

Unit-cell length a length_a	88.087 Å
Unit-cell length b length_b	90.841 Å
Unit-cell length c length_c	105.010 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.160 Å
Low-resolution limit resolution_low	16.440 Å
R factor r_factor	0.1970
R_work r_work	0.1950
R_free r_free	0.2410

fit	/app/data/saxs_computation/b5/6b5q/6b5q.fit
pddf	/app/data/pr_computation/b5/6b5q/6b5q.pr.out
profile	/app/data/saxs_computation/b5/6b5q/6b5q.dat

DCN1 bound to 38

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

DCN1-like protein 1

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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)