4ypg

Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody

Method: X-RAY DIFFRACTION D_max: 148.7 Å Quality: GOOD

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

Sifalimumab light chain

Homo sapiens

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 21–235	Not recorded	Sifalimumab heavy chain × 1 Interferon alpha-2 × 1 （P01563） NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.01 M NiCl2, 0.1 M Tris HCl	Resolution 3.00 Å R-free 0.272
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain L； UniProt 21–235	Not recorded	Sifalimumab heavy chain × 1 Interferon alpha-2 × 1 （P01563） NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.01 M NiCl2, 0.1 M Tris HCl	Resolution 3.00 Å R-free 0.272

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 4YPG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AGJ Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody Deposited 2005-07-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 21–235（215 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 15000-20000, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.60 Å R-free 0.279
6MYY Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map Deposited 2018-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01 Chain F 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01 Chain L 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6MZJ Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs bound, sharpened map Deposited 2018-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 127–235（109 aa） Fragment：germline VK3-11 with the mature CDRL3 of VRC01 Chain L 127–235（109 aa） Fragment：germline VK3-11 with the mature CDRL3 of VRC01	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6UDK HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074 Deposited 2019-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain E 122–235（114 aa） Chain L 122–235（114 aa） Chain N 122–235（114 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；0 blot force, 3.5 second blot time, 3 uL sample added to freshly glow-discharged grids	Resolution 3.90 Å
8QH0 Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194 Deposited 2023-09-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 21–234（214 aa）	Not recorded	PRO PROLINE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% PEG 3350, 0.2 M lithium citrate	Resolution 1.87 Å R-free 0.209
8QH1 Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194 Deposited 2023-09-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 21–235（215 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M sodium malonate	Resolution 2.65 Å R-free 0.232

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

View Construct and Data Evidence

UniProt name	Q6PJF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–215； UniProt 21–235 Author chain L； PDBConstruct 1–215； UniProt 21–235

Interferon alpha-2

Homo sapiens

UniProt P01563

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 24–182	Not recorded	Sifalimumab light chain × 1 （Q6PJF2） Sifalimumab heavy chain × 1 NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.01 M NiCl2, 0.1 M Tris HCl	Resolution 3.00 Å R-free 0.272
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 24–182	Not recorded	Sifalimumab light chain × 1 （Q6PJF2） Sifalimumab heavy chain × 1 NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.01 M NiCl2, 0.1 M Tris HCl	Resolution 3.00 Å R-free 0.272

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4YPG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ITF INTERFERON ALPHA-2A, NMR, 24 STRUCTURES Deposited 1997-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–188（165 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.4；298 K	Resolution not provided
1RH2 RECOMBINANT HUMAN INTERFERON-ALPHA 2B Deposited 1996-11-07	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 24–188（165 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions macroseeding；pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 40MM ZINC ACETATE, 30MM CACODYLATE, PH 5.6; MACRO SEEDING WAS PERFORMED TO GET REASONABLE SIZE CRYSTALS., macroseeding	Resolution 2.90 Å R-free 0.311
1RH2 RECOMBINANT HUMAN INTERFERON-ALPHA 2B Deposited 1996-11-07	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 24–188（165 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions macroseeding；pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 40MM ZINC ACETATE, 30MM CACODYLATE, PH 5.6; MACRO SEEDING WAS PERFORMED TO GET REASONABLE SIZE CRYSTALS., macroseeding	Resolution 2.90 Å R-free 0.311
1RH2 RECOMBINANT HUMAN INTERFERON-ALPHA 2B Deposited 1996-11-07	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 24–188（165 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions macroseeding；pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 40MM ZINC ACETATE, 30MM CACODYLATE, PH 5.6; MACRO SEEDING WAS PERFORMED TO GET REASONABLE SIZE CRYSTALS., macroseeding	Resolution 2.90 Å R-free 0.311
1RH2 RECOMBINANT HUMAN INTERFERON-ALPHA 2B Deposited 1996-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 24–188（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions macroseeding；pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 40MM ZINC ACETATE, 30MM CACODYLATE, PH 5.6; MACRO SEEDING WAS PERFORMED TO GET REASONABLE SIZE CRYSTALS., macroseeding	Resolution 2.90 Å R-free 0.311
1RH2 RECOMBINANT HUMAN INTERFERON-ALPHA 2B Deposited 1996-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 24–188（165 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions macroseeding；pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 40MM ZINC ACETATE, 30MM CACODYLATE, PH 5.6; MACRO SEEDING WAS PERFORMED TO GET REASONABLE SIZE CRYSTALS., macroseeding	Resolution 2.90 Å R-free 0.311
1RH2 RECOMBINANT HUMAN INTERFERON-ALPHA 2B Deposited 1996-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 24–188（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions macroseeding；pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 40MM ZINC ACETATE, 30MM CACODYLATE, PH 5.6; MACRO SEEDING WAS PERFORMED TO GET REASONABLE SIZE CRYSTALS., macroseeding	Resolution 2.90 Å R-free 0.311
2HYM NMR based Docking Model of the Complex between the Human Type I Interferon Receptor and Human Interferon alpha-2 Deposited 2006-08-07	Different construct 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 B 24–188（165 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；308 K；Ionic strength (raw mmCIF value) 20 mM deuterated tris buffer；Pressure ambient NMR sample composition 0.3 mM Interferon-alpha2 (D,15N), 90% D2O, 10% H2O, 20 mM deuterated tris buffer, 0.02% NaN3 \| 90% D2O, 10% H2O NMR sample composition 0.3 mM Interferon-alpha2 (D,15N, 13C), 5% D2O, 95% H2O, 20 mM deuterated tris buffer, 0.02% NaN3 \| 5% D2O, 95% H2O NMR sample composition 0.3 mM Interferon-alpha2 (D,15N), 5% D2O, 95% H2O, 20 mM deuterated tris buffer, 0.02% NaN3 \| 5% D2O, 95% H2O	Resolution not provided
2KZ1 Inter-molecular interactions in a 44 kDa interferon-receptor complex detected by asymmetric back-protonation and 2D NOESY Deposited 2010-06-10	Different construct 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 24–188（165 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；305 K；Ionic strength (raw mmCIF value) 25；Pressure ambient NMR sample composition 0.25 mM [U-99% 2H] Interferon alpha, 0.25 mM [U-99% 2H] Soluble IFN alpha/beta receptor, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.25 MM [U-99% 2H, 1H-K,R,L,A,M] INTERFERON ALPHA2, 0.25 MM [U-99% 2H, 1H-H,F,W] SOLUBLE IFN ALPHA/BETA RECEPTOR, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.25 MM [U-99% 2H, 1H-L] INTERFERON ALPHA2, 0.25 MM [U-99% 2H, 1H-H,W] SOLUBLE IFN ALPHA/BETA RECEPTOR, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.25 MM [15N] INTERFERON ALPHA2, 0.25 MM [1H] SOLUBLE IFN ALPHA/BETA RECEPTOR, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.25 MM [1H] INTERFERON ALPHA2, 0.25 MM [15N] SOLUBLE IFN ALPHA/BETA RECEPTOR, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2LAG Structure of the 44 kDa complex of interferon-alpha2 with the extracellular part of IFNAR2 obtained by 2D-double difference NOESY Deposited 2011-03-13	Different construct 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 24–188（165 aa） Fragment：Extracellular domain residues 28-237	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；305 K；Ionic strength (raw mmCIF value) 25；Pressure ambient NMR sample composition 0.25 mM [U-99% 2H] Interferon alpha/beta receptor 2, 0.25 mM [U-99% 2H] Interferon alpha-2, 100% D2O \| 100% D2O	Resolution not provided
2LMS A single GalNAc residue on Threonine-106 modifies the dynamics and the structure of Interferon alpha-2a around the glycosylation site Deposited 2011-12-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–188（165 aa）	Not recorded	A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1	SOLUTION NMR NMR measurement conditions pH 3.5；298.15 K；Ionic strength (raw mmCIF value) 25；Pressure ambient NMR sample composition 0.85 mM [U-100% 13C; U-100% 15N] Interferon Alpha-2a (O-glycosylated), 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.87 mM [U-100% 13C; U-100% 15N] Interferon Alpha-2a (O-glycosylated), 100% D2O \| 100% D2O	Resolution not provided
3S9D binary complex between IFNa2 and IFNAR2 Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–188（165 aa） Fragment：IFNa2 (UNP Residues 24-188)	Mutation：H57A, E58A, Q61A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；20% (w/v) PEG 3350, 200 mM NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.233
3S9D binary complex between IFNa2 and IFNAR2 Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 24–188（165 aa） Fragment：IFNa2 (UNP Residues 24-188)	Mutation：H57A, E58A, Q61A	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；20% (w/v) PEG 3350, 200 mM NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.233
4Z5R Rontalizumab Fab bound to Interferon-a2 Deposited 2015-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 24–188（165 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, 1% dioxane	Resolution 3.00 Å R-free 0.251
4Z5R Rontalizumab Fab bound to Interferon-a2 Deposited 2015-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 24–188（165 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, 1% dioxane	Resolution 3.00 Å R-free 0.251
4Z5R Rontalizumab Fab bound to Interferon-a2 Deposited 2015-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 24–188（165 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, 1% dioxane	Resolution 3.00 Å R-free 0.251
4Z5R Rontalizumab Fab bound to Interferon-a2 Deposited 2015-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 24–188（165 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, 1% dioxane	Resolution 3.00 Å R-free 0.251
4Z5R Rontalizumab Fab bound to Interferon-a2 Deposited 2015-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 24–188（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, 1% dioxane	Resolution 3.00 Å R-free 0.251
4Z5R Rontalizumab Fab bound to Interferon-a2 Deposited 2015-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 24–188（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, 1% dioxane	Resolution 3.00 Å R-free 0.251
4Z5R Rontalizumab Fab bound to Interferon-a2 Deposited 2015-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 24–188（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, 1% dioxane	Resolution 3.00 Å R-free 0.251
4Z5R Rontalizumab Fab bound to Interferon-a2 Deposited 2015-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 24–188（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, 1% dioxane	Resolution 3.00 Å R-free 0.251
9GVL type-I interferons autoantibody pmab15 in complex with Interferon alpha-2 Deposited 2024-09-25	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 A 24–188（165 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；0.2 M (NH4)2SO4 0.1 M NaAcetate pH 4.6 30 %w/w PEG 2000 MME	Resolution 2.01 Å R-free 0.270
9GVL type-I interferons autoantibody pmab15 in complex with Interferon alpha-2 Deposited 2024-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–188（165 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；0.2 M (NH4)2SO4 0.1 M NaAcetate pH 4.6 30 %w/w PEG 2000 MME	Resolution 2.01 Å R-free 0.270
9GVO type-I interferons autoantibodies pmab15 and pmab14 in complex with Interferon alpha-2 Deposited 2024-09-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–188（165 aa）	Not recorded	GOL GLYCEROL × 6 PO4 PHOSPHATE ION × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M Hepes pH 7.5 0.8 M Na2H2PO4 0.8 M KH2PO4	Resolution 1.81 Å R-free 0.215
9GW5 type-I interferon autoantibodies pmab3, pmab19 and pmab14 in complex with Interferon alpha-2 Deposited 2024-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 24–188（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M Hepes pH 7.5 1.9 (NH4)2SO4	Resolution 4.00 Å R-free 0.324

11 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IFNA2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–161； UniProt 24–182 Author chain D； PDBConstruct 3–161； UniProt 24–182

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ypg
Deposition date deposition_date	2015-03-12
Structure title title	Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody
Keywords keywords	therapeutic mAb, IFN-alpha2A, IMMUNE SYSTEM; IMMUNE SYSTEM
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	47.21 Å
Radius of gyration Rg (electron density) rg_electron	47.31 Å
Forward intensity I(0) i0	255013000.00
Molecular weight molecular_weight	130670.0 kDa
Excluded volume excluded_volume	162890 Å³
Envelope volume envelope_volume	237760 Å³
Hydration-shell volume shell_volume	42136 Å³
Envelope diameter envelope_diameter	143.6 Å
Shell Rg shell_rg	51.76 Å
Envelope Rg envelope_rg	45.36 Å
Shape Rg shape_rg	47.29 Å
Total Rg total_rg	47.59 Å
Total atoms total_atoms	9172
Residues n_residues	1188
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	148.7 Å
Rg (real space) rg_real	47.42 Å
Rg uncertainty (real space) rg_real_error	1.66 Å
I(0) (real space) i0_real	2.5500e+08
I(0) uncertainty (real space) i0_real_error	4.8220e+06
Rg (reciprocal space) rg_reciprocal	47.21 Å
I(0) (reciprocal space) i0_reciprocal	254900000.0000
Solution quality estimate total_estimate	0.8120
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.5 Å
Skewness Skewness skewness	0.175
Kurtosis Kurtosis kurtosis	-1.042
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14790000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.744; Smooth: 0.576

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Sifalimumab light chain
Molecular weight formula_weight	23432.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,L
Atom count atom_count	9219

EIVLTQSPGTLSLSPGERATLSCRASQSVSSTYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	homo sapiens

Entity 2 Entity 2 polymer

Description description	Sifalimumab heavy chain
Molecular weight formula_weight	23217.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H

QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYSISWVRQAPGQGLEWMGWISVYNGNTNYAQKFQGRVTMTTDTSTSTAYLELRSLRSDDTAVYYCARDPIAAGYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

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	homo sapiens

Entity 3 Entity 3 polymer

Description description	Interferon alpha-2
Molecular weight formula_weight	18749.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TSCDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEFGNQFQKAETIPVLHEMIQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACVIQGVGVTETPLMKEDSILAVRKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQE

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	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	47

▼

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d4ypga1
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.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4ypga2
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)

Domain ID domain_id	d4ypgb_
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	d4ypgc1
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.3 — Interferons/interleukin-10 (IL-10)

Domain ID domain_id	d4ypgc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ypgd1
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.3 — Interferons/interleukin-10 (IL-10)

Domain ID domain_id	d4ypgd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ypgh_
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	d4ypgl1
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.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4ypgl2
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 (10 domains)

Domain ID domain_id	4ypgA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ypgA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ypgB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ypgB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ypgC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4ypgD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4ypgH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ypgH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ypgL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ypgL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	134.820 Å
Unit-cell length b length_b	153.260 Å
Unit-cell length c length_c	163.490 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2094
R_work r_work	0.2061
R_free r_free	0.2717

fit	/app/data/saxs_computation/yp/4ypg/4ypg.fit
pddf	/app/data/pr_computation/yp/4ypg/4ypg.pr.out
profile	/app/data/saxs_computation/yp/4ypg/4ypg.dat

Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody

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

Sifalimumab light chain

State in the Current Structure

Other States of the Same Protein in the Database

Interferon alpha-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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)