SAXSdb — 1y16

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

Major prion protein

Mus musculus

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 120–231	Fragment：C-terminal domain Mutation：S170N, N174T	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 4.5；293 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition：1mM mprp(121-213) S170N,N174T U-15N,13C;10mM acetate \| 90% H2O/10% D2O	Resolution not provided

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 1Y16	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AG2 PRION PROTEIN DOMAIN PRP(121-231) FROM MOUSE, NMR, 2 MINIMIZED AVERAGE STRUCTURE Deposited 1997-03-31	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 123–225（103 aa） Fragment：DOMAIN 121 - 231	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；293 K	Resolution not provided
1XYX mouse prion protein fragment 121-231 Deposited 2004-11-11	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–231（112 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；293 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition 1mM mPrP(121-231) U-15N,13C; 10mM acetate \| 90% H2O/10% D2O	Resolution not provided
1Y15 Mouse Prion Protein with mutation N174T Deposited 2004-11-17	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–231（112 aa） Fragment：C-terminal domain	Mutation：N174T	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；293 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition 1mM mPrP(121-231) U-15N,13C; 10mM acetate \| 90% H2O/10% D2O	Resolution not provided
2K5O Mouse Prion Protein (121-231) with Mutation S170N Deposited 2008-06-30	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–231（112 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；298.2 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient NMR sample composition 0.4mM [U-99% 13C; U-99% 15N] Prion Protein, 10% D2O, 90% H2O, 10mM [U-2H] sodium acetate, 0.02% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KFM Mouse Prion Protein (121-231) with Mutations Y225A and Y226A Deposited 2009-02-24	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–231（112 aa）	Mutation：Y225A,Y226A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；293.1 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient NMR sample composition 10 mM [U-100% 2H] sodium acetate-1, 2 mM [U-99% 13C; U-99% 15N] entity-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KFO Mouse Prion Protein (121-231) with Mutation V166A Deposited 2009-02-24	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–231（112 aa）	Mutation：V166A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；293.1 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient NMR sample composition 1.4 mM [U-99% 13C; U-99% 15N] protein, 10 mM [U-100% 2H] sodium acetate, 0.02 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KU5 Mouse Prion Protein (121-231) with mutation D167S Deposited 2010-02-12	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–231（112 aa） Fragment：UNP residues 119-231	Mutation：D167S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 10；298 K；Pressure ambient NMR sample composition 10 mM [U-2H] sodium acetate-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KU6 Mouse Prion Protein (121-231) with mutations D167S and N173K Deposited 2010-02-12	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–231（112 aa） Fragment：UNP residues 119-231	Mutation：D167S, N173K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 10；298 K；Pressure ambient NMR sample composition 10 mM [U-2H] sodium acetate-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3NVG MIHFGN segment 137-142 from mouse prion Deposited 2010-07-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 137–142（6 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；100mM HEPES 7.5, vapor diffusion, hanging drop, temperature 298K	Resolution 1.48 Å R-free 0.205
3NVH MIHFGND segment 137-143 from mouse prion Deposited 2010-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 137–143（7 aa）	Not recorded	TFA trifluoroacetic acid × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100mM HEPES ph 7.0, 10% PEG 1200, vapor diffusion, hanging drop, temperature 298K	Resolution 1.61 Å R-free 0.197
4H88 Structure of POM1 FAB fragment complexed with mouse PrPc Fragment 120-230 Deposited 2012-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 120–230（111 aa） Fragment：C-TERM FRAGMENT	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% PEG3350, 0.1 M BIS-TRIS, 0.2 M lithium sulphate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.234
4J8R Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment Deposited 2013-02-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 67–82（16 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；28% PEG 1000, 0.1M HEPES, 0.2M Calcium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.257
4J8R Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment Deposited 2013-02-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 67–82（16 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；28% PEG 1000, 0.1M HEPES, 0.2M Calcium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.257
4MA7 Crystal structure of mouse prion protein complexed with Promazine Deposited 2013-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 116–229（114 aa） Fragment：UNP residues 116-229	Not recorded	P2Z Promazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% PEG3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.97 Å R-free 0.247
4MA8 Crystal structure of mouse prion protein complexed with Chlorpromazine Deposited 2013-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 116–229（114 aa） Fragment：UNP residues 116-229	Not recorded	Z80 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% PEG3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.236
6AQ7 Structure of POM6 FAB fragment complexed with mouse PrPc Deposited 2017-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 127–225（99 aa） Fragment：UNP residues 127-225	Not recorded	GOL GLYCEROL × 2 TCE 3,3',3''-phosphanetriyltripropanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M Sodium malonate pH 7.0, 12% PEG8000 along with 5mM TCEP, 5mM Praseodymium acetate and ethanol	Resolution 1.83 Å R-free 0.230
6HER Mouse prion protein in complex with Nanobody 484 Deposited 2018-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 117–226（110 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris pH 8, 1.5 M ammonium sulfate	Resolution 1.20 Å R-free 0.195
6HHD Mouse Prion Protein in complex with Nanobody 484 Deposited 2018-08-28	Different construct Different mutation/modification 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 A 118–225（108 aa） Chain C 118–224（107 aa）	Not recorded	CL CHLORIDE ION × 3 SO4 SULFATE ION × 4 GOL GLYCEROL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.15 M ammonium sulfate, 0.1 M MES pH6.0, 15% w/v PEG 40000.	Resolution 2.10 Å R-free 0.245
7QIG Infectious mouse-adapted RML scrapie prion fibril purified from terminally-infected mouse brains Deposited 2021-12-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 94–225（132 aa） Chain B 94–225（132 aa） Chain C 94–225（132 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7RVD Segment from the mouse/cow prion protein 168-176 QYSNQNNFV Deposited 2021-08-18	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 167–175（9 aa） Fragment：UNP residues 167-175	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.5 M zinc acetate, 15% ethanol, 0.2 M MES, pH 6	Resolution 1.00 Å R-free 0.250
7TD6 aRML prion fibril Deposited 2021-12-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain 1 1–254（254 aa） Chain A 1–254（254 aa） Chain B 1–254（254 aa） Chain C 1–254（254 aa） Chain D 1–254（254 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8A00 Infectious mouse-adapted ME7 scrapie prion fibril purified from terminally-infected mouse brains Deposited 2022-05-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 94–229（136 aa） Chain B 94–229（136 aa） Chain C 94–229（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8DJA Cryo-EM structure of mouse PrP23-144 amyloid fibrils (polymorph 1) Deposited 2022-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric	Chain A 23–143（121 aa） Chain B 23–143（121 aa） Chain C 23–143（121 aa） Chain D 23–143（121 aa） Chain E 23–143（121 aa） Chain F 23–143（121 aa） Chain G 23–143（121 aa） Chain H 23–143（121 aa） Chain I 23–143（121 aa） Chain J 23–143（121 aa） Chain K 23–143（121 aa） Chain L 23–143（121 aa） Chain M 23–143（121 aa） Chain N 23–143（121 aa） Chain O 23–143（121 aa） Chain P 23–143（121 aa） Chain Q 23–143（121 aa） Chain R 23–143（121 aa） Chain S 23–143（121 aa） Chain T 23–143（121 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.92 Å
8EFU a22L prion fibril Deposited 2022-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–231（231 aa） Chain B 1–231（231 aa） Chain C 1–231（231 aa） Chain D 1–231（231 aa） Chain E 1–231（231 aa）	Mutation：S233Stop Mutation：S233Stop Mutation：S233Stop Mutation：S233Stop Mutation：S233Stop	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；Sample suspended in 20 mM Tris pH 7.4, 100 mM containing 0.02% amphipol 8-35 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

23 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRIO_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 120–231

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	1y16
Deposition date deposition_date	2004-11-17
Structure title title	mouse prion protein with mutations S170N and N174T
Keywords keywords	prion protein, PrP, PrnP, TSE, CWD, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.36 Å
Radius of gyration Rg (electron density) rg_electron	15.07 Å
Forward intensity I(0) i0	1105460000.00
Molecular weight molecular_weight	264920.0 kDa
Excluded volume excluded_volume	323690 Å³
Envelope volume envelope_volume	27187 Å³
Hydration-shell volume shell_volume	14222 Å³
Envelope diameter envelope_diameter	58.7 Å
Shell Rg shell_rg	22.23 Å
Envelope Rg envelope_rg	17.16 Å
Shape Rg shape_rg	15.09 Å
Total Rg total_rg	15.12 Å
Total atoms total_atoms	35880
Residues n_residues	2240
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	51.4 Å
Rg (real space) rg_real	15.41 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.1050e+09
I(0) uncertainty (real space) i0_real_error	1.2230e+07
Rg (reciprocal space) rg_reciprocal	15.40 Å
I(0) (reciprocal space) i0_reciprocal	1105000000.0000
Solution quality estimate total_estimate	0.8718
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.6 Å
Skewness Skewness skewness	0.409
Kurtosis Kurtosis kurtosis	-0.270
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	482600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.985

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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	d1y16a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.6 — Prion-like
Superfamily Superfamily superfamily	d.6.1 — Prion-like
Family Family family	d.6.1.1 — Prion-like

CATH v4.4 (1 domains)

Domain ID domain_id	1y16A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	790 — Major Prion Protein
Homologous superfamily homologous superfamily	10 — Prion/Doppel protein, beta-ribbon domain

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8. Citations (1)

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Description description	Major prion protein
Molecular weight formula_weight	13278.8 kDa
Mutation mutation	S170N, N174T
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	35880

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21

fit	/app/data/saxs_computation/y1/1y16/1y16.fit
pddf	/app/data/pr_computation/y1/1y16/1y16.pr.out
profile	/app/data/saxs_computation/y1/1y16/1y16.dat

mouse prion protein with mutations S170N and N174T

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

Major prion 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

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)