SAXSdb — 9cce

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

Dynorphin A(1-17)

OrganismNot specified

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 D； UniProt 207–223	Not recorded	DYNA_1b7 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1 M Phosphate/citrate pH 4.2 and 40 % v/v PEG 300	Resolution 3.15 Å R-free 0.313
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 207–223	Not recorded	DYNA_1b7 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1 M Phosphate/citrate pH 4.2 and 40 % v/v PEG 300	Resolution 3.15 Å R-free 0.313

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 9CCE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N2F Solution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor Deposited 2015-05-06	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 207–219（13 aa） Fragment：residues 207-219	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；280 K；Pressure ambient NMR sample composition 1 mM [U-15N-GFLI] Dynorphin 1, 150 mM potassium chloride, 40 mM [U-2H] MES, 100 uM DSS, 10 uM KOR, 8 mM DDM, 1.6 mM CHS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-15N-GFLIR; U-13C-R] Dynorphin 1, 150 mM potassium chloride, 40 mM [U-2H] MES, 100 uM DSS, 10 uM KOR, 8 mM DDM, 1.6 mM CHS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8F7W Gi bound kappa-opioid receptor in complex with dynorphin Deposited 2022-11-20	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 P 207–214（8 aa） Fragment：UNP residues 207-214	Not recorded	CLR CHOLESTEROL × 3 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å
8VJU Structure of Human Neurolysin in complex with dynorphin A13 peptide Deposited 2024-01-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 207–219（13 aa）	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5	Resolution 1.99 Å R-free 0.218
8VJV Structure of Human Neurolysin in complex with dynorphin A8(1-8) peptide Deposited 2024-01-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 207–214（8 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5	Resolution 2.12 Å R-free 0.249
9CCF Crystal Structure of DA7-2 Deposited 2024-06-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 207–223（17 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6 and 25% (v/v) PEG 550 MME	Resolution 4.00 Å R-free 0.296
9CCF Crystal Structure of DA7-2 Deposited 2024-06-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 207–223（17 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6 and 25% (v/v) PEG 550 MME	Resolution 4.00 Å R-free 0.296
9L60 Gi-bound kappa opioid receptor in complex with dynorphin and positive allosteric modulator MPAM-15 Deposited 2024-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 207–219（13 aa）	Not recorded	CLR CHOLESTEROL × 2 A1D6C 9-[5-(3-chlorophenyl)furan-2-yl]-3,3,6,6-tetramethyl-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDYN_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–17； UniProt 207–223 Author chain D； PDBConstruct 1–17； UniProt 207–223

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	9cce
Deposition date deposition_date	2024-06-21
最后修订 last_revision	2025-08-13
Structure title title	structure of DYNA_1b7
Keywords keywords	de novo design, deep learning, disorder peptide, protein-peptide complex, DE NOVO PROTEIN; DE NOVO 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	26.24 Å
Radius of gyration Rg (electron density) rg_electron	25.24 Å
Forward intensity I(0) i0	36040500.00
Molecular weight molecular_weight	47613.0 kDa
Excluded volume excluded_volume	60428 Å³
Envelope volume envelope_volume	75804 Å³
Hydration-shell volume shell_volume	25711 Å³
Envelope diameter envelope_diameter	84.9 Å
Shell Rg shell_rg	31.83 Å
Envelope Rg envelope_rg	25.32 Å
Shape Rg shape_rg	25.24 Å
Total Rg total_rg	26.05 Å
Total atoms total_atoms	3355
Residues n_residues	410
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	82.6 Å
Rg (real space) rg_real	26.29 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	3.6040e+07
I(0) uncertainty (real space) i0_real_error	4.9870e+05
Rg (reciprocal space) rg_reciprocal	26.28 Å
I(0) (reciprocal space) i0_reciprocal	36040000.0000
Solution quality estimate total_estimate	0.8891
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.5 Å
Skewness Skewness skewness	0.370
Kurtosis Kurtosis kurtosis	-0.490
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6788000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.820

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	DYNA_1b7
Molecular weight formula_weight	25195.5 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	3355

MSGKEEEIEKEFEEKKKIIEENLKEAEEEGEEEAAEKLKEALKKLEEAIKLHREGANPVEVELEEVTAIILNNLAVLLREGEEELAKELEKAIKLLEEKKDAPEEERLKAIAIAIIRSVLVLIKWEGGKDEETIEEIEEILENRENLSLEELREAYVRAEIAYLIESGIDPEAAKKVREKYERGAPLEELLKDIEKIEKEAKKREEEKKGSHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Dynorphin A(1-17)
Molecular weight formula_weight	2152.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

YGGFLRRIRPKLKWDNQ

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8. Citations (1)

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Unit-cell length a length_a	44.433 Å
Unit-cell length b length_b	67.783 Å
Unit-cell length c length_c	68.360 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	28.840 Å
R factor r_factor	0.2626
R_work r_work	0.2571
R_free r_free	0.3130

fit	/app/data/saxs_computation/cc/9cce/9cce.fit
pddf	/app/data/pr_computation/cc/9cce/9cce.pr.out
profile	/app/data/saxs_computation/cc/9cce/9cce.dat

structure of DYNA_1b7

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

Dynorphin A(1-17)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)