SAXSdb — 2vxq

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

POLLEN ALLERGEN PHL P 2

PHLEUM PRATENSE

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 27–122	Fragment：RESIDUES 27-122	FAB × 1 FAB × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；HANGING DROP DIFFUSION, 1 MICROL PROTEIN (IN 30 MM HEPES, 0.15 M NACL PH 6.8) MIXED WITH 1 MICROL RESERVOIR (20% PEG 3350, 0.2 M NAF)	Resolution 1.90 Å R-free 0.226

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 2VXQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BMW A fibronectin type III fold in plant allergens: The solution structure of Phl PII from timothy grass pollen, NMR, 38 STRUCTURES Deposited 1998-07-27	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 27–122（96 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 10 mM PHOSPHATE BUFFER；Pressure 1 NMR sample composition H2O	Resolution not provided
1WHO ALLERGEN PHL P 2 Deposited 1997-04-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–122（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；CRYSTALLIZED FROM 24% PEG 4000 SOLUTION., pH 4.6	Resolution 1.90 Å
1WHP ALLERGEN PHL P 2 Deposited 1997-04-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–122（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；CRYSTALLIZED FROM 24% PEG 4000 SOLUTION., pH 4.6	Resolution 3.00 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MPAP2_PHLPR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–96； UniProt 27–122

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	2vxq
Deposition date deposition_date	2008-07-08
Structure title title	Crystal structure of the major grass pollen allergen Phl p 2 in complex with its specific IgE-Fab
Keywords keywords	RECEPTOR, SECRETED, RPHL P 2, ALLERGEN, ALLERGEN-IGE FAB COMPLEX, RECOMBINANT GRASS POLLEN ALLERGEN; ALLERGEN
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	28.08 Å
Radius of gyration Rg (electron density) rg_electron	27.72 Å
Forward intensity I(0) i0	52214700.00
Molecular weight molecular_weight	56267.0 kDa
Excluded volume excluded_volume	70256 Å³
Envelope volume envelope_volume	86494 Å³
Hydration-shell volume shell_volume	27490 Å³
Envelope diameter envelope_diameter	106.4 Å
Shell Rg shell_rg	33.23 Å
Envelope Rg envelope_rg	27.64 Å
Shape Rg shape_rg	27.70 Å
Total Rg total_rg	28.34 Å
Total atoms total_atoms	3967
Residues n_residues	518
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	96.8 Å
Rg (real space) rg_real	28.30 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	5.2210e+07
I(0) uncertainty (real space) i0_real_error	8.0960e+05
Rg (reciprocal space) rg_reciprocal	28.24 Å
I(0) (reciprocal space) i0_reciprocal	52210000.0000
Solution quality estimate total_estimate	0.8559
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.531
Kurtosis Kurtosis kurtosis	-0.165
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10370000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.838; Smooth: 0.909

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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	POLLEN ALLERGEN PHL P 2
Molecular weight formula_weight	10828.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4491

VPKVTFTVEKGSNEKHLAVLVKYEGDTMAEVELREHGSDEWVAMTKGEGGVWTFDSEEPLQGPFNFRFLTEKGMKNVFDDVVPEKYTIGATYAPEE

来源 Source

来源生物 organism	PHLEUM PRATENSE
通用名 common_name	COMMON TIMOTHY
NCBI Class编号 ncbi_taxonomy_id	15957
宿主生物 host_organism	ESCHERICHIA COLI BL21

Entity 2 Entity 2 polymer

Description description	FAB
Molecular weight formula_weight	22976.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

VQLLESGPGLVKPAQTLSLSCAVSGGSIRSGGYYWSWIRQHPGKGLEWIGYIYHSGNTYYNPSLKSRIAMSVDTSENKFSLRLNSVTAADTAVYYCARLDGYTLDIWGQGTLVTVSSSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP

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	CRICETULUS GRISEUS

Entity 3 Entity 3 polymer

Description description	FAB
Molecular weight formula_weight	23445.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

EIEMTQSPSSLSASVGDRVTISCRASQRINTYLNWYQHKPGKAPKLLIYAASSLQSGVPSRFSGSGYGTDFTLTISSLQPEDFASYYCQESLSASYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	CRICETULUS GRISEUS

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	524

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2vxqa_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.3 — PHL pollen allergen
Family Family family	b.7.3.1 — PHL pollen allergen

Domain ID domain_id	d2vxqh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2vxql1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2vxql2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	2vxqA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	760 — Expansin, cellulose-binding-like domain

Domain ID domain_id	2vxqH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2vxqH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2vxqL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2vxqL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	105.437 Å
Unit-cell length b length_b	105.437 Å
Unit-cell length c length_c	110.225 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	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1790
R_work r_work	0.1770
R_free r_free	0.2260

fit	/app/data/saxs_computation/vx/2vxq/2vxq.fit
pddf	/app/data/pr_computation/vx/2vxq/2vxq.pr.out
profile	/app/data/saxs_computation/vx/2vxq/2vxq.dat

Crystal structure of the major grass pollen allergen Phl p 2 in complex with its specific IgE-Fab

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

POLLEN ALLERGEN PHL P 2

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

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)