SAXSdb — 5vpk

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

Der f 1 variant

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 83–305	Fragment：SEQUENCE DATABASE RESIDUES 99-321	SO4 SULFATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 10.5；293 K；PROTEIN SOLUTION: 0.5M L-ARGININE, 0.12M LI SULFATE, 0.004M EDTA, 0.1M CAPS, PH 10.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 10.50	Resolution 2.00 Å R-free 0.210
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 83–305	Fragment：SEQUENCE DATABASE RESIDUES 99-321	SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 10.5；293 K；PROTEIN SOLUTION: 0.5M L-ARGININE, 0.12M LI SULFATE, 0.004M EDTA, 0.1M CAPS, PH 10.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 10.50	Resolution 2.00 Å R-free 0.210
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 83–305	Fragment：SEQUENCE DATABASE RESIDUES 99-321	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 10.5；293 K；PROTEIN SOLUTION: 0.5M L-ARGININE, 0.12M LI SULFATE, 0.004M EDTA, 0.1M CAPS, PH 10.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 10.50	Resolution 2.00 Å R-free 0.210

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 5VPK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VPL CRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1 Deposited 2017-05-05	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 83–305（223 aa） Fragment：UNP RESIDUES 99-321	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.1M HEPES, 18% W/V PEG12K, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.90 Å R-free 0.194

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	I2CMD3_DERFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–223； UniProt 83–305 Author chain B； PDBConstruct 1–223； UniProt 83–305 Author chain C； PDBConstruct 1–223； UniProt 83–305

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	5vpk
Deposition date deposition_date	2017-05-05
Structure title title	CRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1
Keywords keywords	ALLERGY, DUST MITES, ALLERGEN, GLYCOPROTEIN, HYDROLASE, PROTEASE, SECRETED, THIOL PROTEASE, ZYMOGEN; 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	28.89 Å
Radius of gyration Rg (electron density) rg_electron	28.09 Å
Forward intensity I(0) i0	102802000.00
Molecular weight molecular_weight	75405.0 kDa
Excluded volume excluded_volume	92374 Å³
Envelope volume envelope_volume	116950 Å³
Hydration-shell volume shell_volume	34686 Å³
Envelope diameter envelope_diameter	93.1 Å
Shell Rg shell_rg	35.41 Å
Envelope Rg envelope_rg	27.90 Å
Shape Rg shape_rg	28.09 Å
Total Rg total_rg	28.78 Å
Total atoms total_atoms	5296
Residues n_residues	669
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	88.7 Å
Rg (real space) rg_real	28.81 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.0280e+08
I(0) uncertainty (real space) i0_real_error	1.6930e+06
Rg (reciprocal space) rg_reciprocal	28.85 Å
I(0) (reciprocal space) i0_reciprocal	102800000.0000
Solution quality estimate total_estimate	0.9091
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.9 Å
Skewness Skewness skewness	0.208
Kurtosis Kurtosis kurtosis	-0.544
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25210000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.924

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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	Der f 1 variant
Molecular weight formula_weight	25171.0 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5614

TSACRINSVNVPSELDLRSLRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNTSLDLSEQELVDCASQHGCHGDTIPRGIEYIQQNGVVEERSYPYVAREQQCRRPNSQHYGISNYCQIYPPDVKQIREALTQTHTAIAVIIGIKDLRAFQHYDGRTIIQHDNGYQPNYHAVNIVGYGSTQGVDYWIVRNSWDTTWGDSGYGYFQAGNNLMMIEQYPYVVIM

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
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	289

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5vpkA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	5vpkB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	5vpkC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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8. Citations (1)

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Unit-cell length a length_a	91.159 Å
Unit-cell length b length_b	91.159 Å
Unit-cell length c length_c	77.743 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	12

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	36.100 Å
R factor r_factor	0.1810
R_work r_work	0.1795
R_free r_free	0.2101

fit	/app/data/saxs_computation/vp/5vpk/5vpk.fit
pddf	/app/data/pr_computation/vp/5vpk/5vpk.pr.out
profile	/app/data/saxs_computation/vp/5vpk/5vpk.dat

CRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1

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

Der f 1 variant

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