← Back to search
5vpl

CRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1

Method: X-RAY DIFFRACTION Dmax: 114.6 Å Quality: GOOD
▼

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

Der f 1 variant

OrganismNot specified

UniProt I2CMD3

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 83–305 Fragment：UNP RESIDUES 99-321 4C1 - LIGHT CHAIN × 1 （Q7TS98） 4C1 - HEAVY CHAIN × 1 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

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 5VPL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5VPK CRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1 Deposited 2017-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 83–305（223 aa） Fragment：SEQUENCE DATABASE RESIDUES 99-321
Not recorded 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
5VPK CRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1 Deposited 2017-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 83–305（223 aa） Fragment：SEQUENCE DATABASE RESIDUES 99-321
Not recorded 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
5VPK CRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1 Deposited 2017-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 83–305（223 aa） Fragment：SEQUENCE DATABASE RESIDUES 99-321
Not recorded No recorded non-water small molecule 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

1 other PDB entries and 3 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

4C1 - LIGHT CHAIN

Mus musculus

UniProt Q7TS98

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 C； UniProt 24–235 Not recorded Der f 1 variant × 1 （I2CMD3） 4C1 - HEAVY CHAIN × 1 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

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 5VPL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Chain L 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded CD CADMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.285
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.285
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded CD CADMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.285
1D5I UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded CD CADMIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；75mM Hepes pH 7.0 9% PEG 4000 150 mM Ammonium Sulfate 20% 1,4 butanediol 100 mM Cadmium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.263
1D6V CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION Deposited 1999-10-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded CD CADMIUM ION × 4 HOP (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；9% polyethylene glycol 4000 250mM ammonium sulfate 80mM Cadmium Chloride 75mM Hepes 20% 1,4 butanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 19K
Resolution 2.00 Å R-free 0.264
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 720 PDB declaration: 720-meric
Chain H 130–234（105 aa） Fragment：SEE REMARK 999
Chain J 130–234（105 aa） Fragment：SEE REMARK 999
Chain L 130–234（105 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer
cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)
Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 130–234（105 aa） Fragment：SEE REMARK 999
Chain J 130–234（105 aa） Fragment：SEE REMARK 999
Chain L 130–234（105 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer
cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)
Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 60 PDB declaration: 60-meric
Chain H 130–234（105 aa） Fragment：SEE REMARK 999
Chain J 130–234（105 aa） Fragment：SEE REMARK 999
Chain L 130–234（105 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer
cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)
Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Heteromer；Protein × 72 PDB declaration: 72-meric
Chain H 130–234（105 aa） Fragment：SEE REMARK 999
Chain J 130–234（105 aa） Fragment：SEE REMARK 999
Chain L 130–234（105 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer
cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)
Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 130–234（105 aa） Fragment：SEE REMARK 999
Chain J 130–234（105 aa） Fragment：SEE REMARK 999
Chain L 130–234（105 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer
cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)
Resolution 21.00 Å
4KVC 2H2 Fab fragment of immature Dengue virus Deposited 2013-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 130–234（105 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；25% PEG 6000 0.1 M MES 0.2M NH4Cl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.31 Å R-free 0.234
5TR8 Crystal structure of vaccine-elicited pan- influenza H1N1 neutralizing murine antibody 441D6. Deposited 2016-10-25 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 L 132–234（103 aa）
Not recorded NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；12% PEG3350, 100 mM HEPES pH 7.5, 5 mM MgCl2, 5mM NiCl2
Resolution 2.01 Å R-free 0.198

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q7TS98_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 2–213； UniProt 24–235

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5vpl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5vpl
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5vpl
Deposition date deposition_date2017-05-05
Structure title titleCRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1
Keywords keywordsCOMPLEX BETWEEN AN ALLERGEN AND FAB FRAGMENT OF 4C1 ANTIBODY, HYDROLASE-IMMUNE SYSTEM COMPLEX; HYDROLASE/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier32.96 Å
Radius of gyration Rg (electron density) rg_electron32.77 Å
Forward intensity I(0) i086956400.00
Molecular weight molecular_weight72842.0 kDa
Excluded volume excluded_volume90469 ų
Envelope volume envelope_volume115660 ų
Hydration-shell volume shell_volume32100 ų
Envelope diameter envelope_diameter115.6 Å
Shell Rg shell_rg36.61 Å
Envelope Rg envelope_rg32.70 Å
Shape Rg shape_rg32.74 Å
Total Rg total_rg33.18 Å
Total atoms total_atoms5124
Residues n_residues650
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax114.6 Å
Rg (real space) rg_real33.41 Å
Rg uncertainty (real space) rg_real_error1.23 Å
I(0) (real space) i0_real8.6960e+07
I(0) uncertainty (real space) i0_real_error1.4630e+06
Rg (reciprocal space) rg_reciprocal33.23 Å
I(0) (reciprocal space) i0_reciprocal86940000.0000
Solution quality estimate total_estimate0.8137
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.0 Å
Skewness Skewness skewness0.581
Kurtosis Kurtosis kurtosis-0.332
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12620000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.696; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.657; Smooth: 0.831
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

▼

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5vplc1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd5vplc2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd5vplc3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id5vplA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id5vplC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5vplC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5vplD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

8. Citations (1)

▶

9. Files and Curves (10)