SAXSdb — 1cdz

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

PROTEIN (DNA-REPAIR PROTEIN XRCC1)

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 538–633	Fragment：C-TERMINAL BRCT DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 3.20 Å R-free 0.266

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 1CDZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XNA NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN Deposited 1999-02-27	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–183（183 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152-183 ARE DISORDERED AND NOT SHOWN.	Mutation：D179E	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure 1 NMR sample composition H2O AND D2O	Resolution not provided
1XNT NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN Deposited 1999-02-27	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–183（183 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152-183 ARE DISORDERED AND NOT SHOWN.	Mutation：D179E	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure 1 NMR sample composition H2O AND D2O	Resolution not provided
2D8M Solution structure of the first BRCT domain of DNA-repair protein XRCC1 Deposited 2005-12-06	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 305–420（116 aa） Fragment：BRCT domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 0.89mM BRCT domain U-15N,13C; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2W3O Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide Deposited 2008-11-13	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 C 515–522（8 aa） Fragment：RESIDUES 515-522	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 0.25 M CACL2, 28% W/V PEG 4000, 0.2 M NDSB-221	Resolution 1.85 Å R-free 0.236
2W3O Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide Deposited 2008-11-13	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 D 515–522（8 aa） Fragment：RESIDUES 515-522	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 0.25 M CACL2, 28% W/V PEG 4000, 0.2 M NDSB-221	Resolution 1.85 Å R-free 0.236
3K75 X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain Deposited 2009-10-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–183（183 aa） Fragment：N-terminal domain (UNP residues 1 to 183)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M Tri-potassium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.95 Å R-free 0.295
3K75 X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain Deposited 2009-10-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–183（183 aa） Fragment：N-terminal domain (UNP residues 1 to 183)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M Tri-potassium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.95 Å R-free 0.295
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.237
3LQC X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain Deposited 2010-02-09	Different construct 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 1–183（183 aa）	Not recorded	NA SODIUM ION × 1 CO3 CARBONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M TRI-POTASSIUM CITRATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.35 Å R-free 0.250
5E6Q Importin alpha binding to XRCC1 NLS peptide Deposited 2015-10-10	Different construct 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 241–276（36 aa） Fragment：UNP residues 241-276	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.5M Ammonium sulfate, 0.1M bis-tris propane	Resolution 2.31 Å R-free 0.208
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 514–522（9 aa） Fragment：UNP residues 514-522	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 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000	Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 514–522（9 aa） Fragment：UNP residues 514-522	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 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000	Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 514–522（9 aa） Fragment：UNP residues 514-522	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 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000	Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 514–522（9 aa） Fragment：UNP residues 514-522	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 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000	Resolution 2.00 Å R-free 0.229
5W7Y Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide Deposited 2017-06-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 514–521（8 aa） Fragment：UNP residues 514-521	Mutation：S518E 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 8.5；293 K；0.6mM APLF 0.6mM XRCC1 peptide 0.1M Tris 30% PEG 1000	Resolution 2.10 Å R-free 0.237
5W7Y Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide Deposited 2017-06-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 514–521（8 aa） Fragment：UNP residues 514-521	Mutation：S518E 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 8.5；293 K；0.6mM APLF 0.6mM XRCC1 peptide 0.1M Tris 30% PEG 1000	Resolution 2.10 Å R-free 0.237

10 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XRCC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–96； UniProt 538–633

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	1cdz
Deposition date deposition_date	1999-03-04
Structure title title	BRCT DOMAIN FROM DNA-REPAIR PROTEIN XRCC1
Keywords keywords	BRCT, BRCA1, XRCC1, PROTEIN-PROTEIN INTERACTION, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	14.50 Å
Radius of gyration Rg (electron density) rg_electron	12.93 Å
Forward intensity I(0) i0	2576160.00
Molecular weight molecular_weight	11386.0 kDa
Excluded volume excluded_volume	14332 Å³
Envelope volume envelope_volume	15676 Å³
Hydration-shell volume shell_volume	10461 Å³
Envelope diameter envelope_diameter	46.6 Å
Shell Rg shell_rg	18.50 Å
Envelope Rg envelope_rg	13.38 Å
Shape Rg shape_rg	12.88 Å
Total Rg total_rg	14.35 Å
Total atoms total_atoms	808
Residues n_residues	96
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	47.5 Å
Rg (real space) rg_real	14.42 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	2.5760e+06
I(0) uncertainty (real space) i0_real_error	2.8830e+04
Rg (reciprocal space) rg_reciprocal	14.43 Å
I(0) (reciprocal space) i0_reciprocal	2576000.0000
Solution quality estimate total_estimate	0.8058
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.9 Å
Skewness Skewness skewness	0.183
Kurtosis Kurtosis kurtosis	-0.265
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	415700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cdza_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.15 — BRCT domain
Superfamily Superfamily superfamily	c.15.1 — BRCT domain
Family Family family	c.15.1.1 — DNA-repair protein XRCC1

CATH v4.4 (1 domains)

Domain ID domain_id	1cdzA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

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8. Citations (1)

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Unit-cell length a length_a	100.800 Å
Unit-cell length b length_b	100.800 Å
Unit-cell length c length_c	72.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2240
R_free r_free	0.2660

Description description	PROTEIN (DNA-REPAIR PROTEIN XRCC1)
Molecular weight formula_weight	11419.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	808

BRCT DOMAIN FROM DNA-REPAIR PROTEIN XRCC1

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

PROTEIN (DNA-REPAIR PROTEIN XRCC1)

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/cd/1cdz/1cdz.fit
pddf	/app/data/pr_computation/cd/1cdz/1cdz.pr.out
profile	/app/data/saxs_computation/cd/1cdz/1cdz.dat