4y5x

Diabody 305 complex with EpoR

Method: X-RAY DIFFRACTION D_max: 205.9 Å Quality: REASONABLE

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

diabody 310 VH domain

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain B； UniProt 1–97 Chain K； UniProt 1–97	Not recorded	diabody 310 VL domain × 2 Erythropoietin receptor × 2 （P19235） PEG DI(HYDROXYETHYL)ETHER × 12 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；sodium citrate, PEG 8000	Resolution 3.15 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 1–97 Chain H； UniProt 1–97	Not recorded	diabody 310 VL domain × 2 Erythropoietin receptor × 2 （P19235） PEG DI(HYDROXYETHYL)ETHER × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；sodium citrate, PEG 8000	Resolution 3.15 Å R-free 0.241

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q5NV67_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–97； UniProt 1–97 Author chain E； PDBConstruct 1–97； UniProt 1–97 Author chain H； PDBConstruct 1–97； UniProt 1–97 Author chain K； PDBConstruct 1–97； UniProt 1–97

Erythropoietin receptor

Homo sapiens

UniProt P19235

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain C； UniProt 32–249 Chain L； UniProt 32–249	Not recorded	diabody 310 VL domain × 2 diabody 310 VH domain × 2 （Q5NV67） PEG DI(HYDROXYETHYL)ETHER × 12 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；sodium citrate, PEG 8000	Resolution 3.15 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain F； UniProt 32–249 Chain I； UniProt 32–249	Not recorded	diabody 310 VL domain × 2 diabody 310 VH domain × 2 （Q5NV67） PEG DI(HYDROXYETHYL)ETHER × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；sodium citrate, PEG 8000	Resolution 3.15 Å R-free 0.241

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4Y5X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CN4 ERYTHROPOIETIN COMPLEXED WITH EXTRACELLULAR DOMAINS OF ERYTHROPOIETIN RECEPTOR Deposited 1999-05-25	Different construct Different mutation/modification 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 25–249（225 aa） Fragment：EXTRACELLULAR LIGAND BINDING DOMAINS Chain B 25–249（225 aa） Fragment：EXTRACELLULAR LIGAND BINDING DOMAINS	Mutation：N52Q, N164Q, A211E Mutation：N52Q, N164Q, A211E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.80 Å R-free 0.336
1EBA COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN INACTIVE PEPTIDE [EMP33] CONTAINS 3,5-DIBROMOTYROSINE IN POSITION 4 (DENOTED DBY) Deposited 1998-10-02	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 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.70 Å R-free 0.299
1EBA COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN INACTIVE PEPTIDE [EMP33] CONTAINS 3,5-DIBROMOTYROSINE IN POSITION 4 (DENOTED DBY) Deposited 1998-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.70 Å R-free 0.299
1EBA COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN INACTIVE PEPTIDE [EMP33] CONTAINS 3,5-DIBROMOTYROSINE IN POSITION 4 (DENOTED DBY) Deposited 1998-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.70 Å R-free 0.299
1EBP COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN AGONIST PEPTIDE [EMP1] Deposited 1996-05-07	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 34–244（211 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–244（211 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.334
1EER CRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS RECEPTOR AT 1.9 ANGSTROMS Deposited 1998-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 31–250（220 aa） Fragment：EXTRACELLULAR DOMAIN Chain C 31–250（220 aa） Fragment：EXTRACELLULAR DOMAIN	Mutation：N52Q, N164Q, A211E Mutation：N52Q, N164Q, A211E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.90 Å R-free 0.318
1ERN NATIVE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] Deposited 1999-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–246（213 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–246（213 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.7；pH 7.7	Resolution 2.40 Å R-free 0.295
2JIX Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor Deposited 2007-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 25–249（225 aa） Fragment：EPO RECEPTOR SOLUBLE DOMAIN, RESIDUES 25-249	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.323
2JIX Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor Deposited 2007-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 25–249（225 aa） Fragment：EPO RECEPTOR SOLUBLE DOMAIN, RESIDUES 25-249	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.323
2JIX Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor Deposited 2007-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 25–249（225 aa） Fragment：EPO RECEPTOR SOLUBLE DOMAIN, RESIDUES 25-249	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.323
2MV6 Solution structure of the transmembrane domain and the juxta-membrane domain of the Erythropoietin Receptor in micelles Deposited 2014-09-23	Different construct Different mutation/modification 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 237–284（48 aa） Fragment：UNP residues 237-284	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；313 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 20 mM sodium phosphate, 10 v/v D2O, 250 mM DPC, 0.5 mM [U-99% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] protein, 10 % D2O, 20 mM sodium phosphate, 200-400 mM DPC, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4Y5V Diabody 305 complex with EpoR Deposited 2015-02-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 32–249（218 aa） Chain F 32–249（218 aa）	Mutation：N52Q, N164Q Mutation：N52Q, N164Q	GOL GLYCEROL × 10 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；HEPES, PEG 4000	Resolution 2.60 Å R-free 0.229
4Y5V Diabody 305 complex with EpoR Deposited 2015-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 32–249（218 aa）	Mutation：N52Q, N164Q	GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；HEPES, PEG 4000	Resolution 2.60 Å R-free 0.229
4Y5Y Diabody 330 complex with EpoR Deposited 2015-02-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 32–249（218 aa） Chain F 32–249（218 aa）	Mutation：N76Q, N188Q, D247L, and L248D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N76Q, N188Q, D247L, and L248D Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；Magnesium chloride, Tris, PEG 8000	Resolution 2.85 Å R-free 0.241
6E2Q Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor Deposited 2018-07-11	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 N 273–338（66 aa） Fragment：UNP residues 273-338	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；100 mM Tris, pH 7.6, 2-4% PEG8000	Resolution 2.65 Å R-free 0.263
6E2Q Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor Deposited 2018-07-11	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 O 273–338（66 aa） Fragment：UNP residues 273-338	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；100 mM Tris, pH 7.6, 2-4% PEG8000	Resolution 2.65 Å R-free 0.263
6E2Q Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor Deposited 2018-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 273–338（66 aa） Fragment：UNP residues 273-338	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；100 mM Tris, pH 7.6, 2-4% PEG8000	Resolution 2.65 Å R-free 0.263
6E2Q Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor Deposited 2018-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 273–338（66 aa） Fragment：UNP residues 273-338	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；100 mM Tris, pH 7.6, 2-4% PEG8000	Resolution 2.65 Å R-free 0.263
6MOE Monomeric DARPin E2 complex with EpoR Deposited 2018-10-04	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 D 32–249（218 aa）	Not recorded	PO4 PHOSPHATE ION × 5 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；295 K；1 M sodium potassium phosphate pH 5.6 Cryoprotected in 25% ethylene glycol	Resolution 2.09 Å R-free 0.230
6MOE Monomeric DARPin E2 complex with EpoR Deposited 2018-10-04	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 32–249（218 aa）	Not recorded	PO4 PHOSPHATE ION × 4 EDO 1,2-ETHANEDIOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；295 K；1 M sodium potassium phosphate pH 5.6 Cryoprotected in 25% ethylene glycol	Resolution 2.09 Å R-free 0.230
6MOF Monomeric DARPin G2 complex with EpoR Deposited 2018-10-04	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 B 32–249（218 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；0.2 M Magnesium chloride, 0.1 M Tris pH 7.0, 10% PEG 8000, 25% ethylene glycol as cryoprotectant	Resolution 2.89 Å R-free 0.266
6MOH Dimeric DARPin C_R3 complex with EpoR Deposited 2018-10-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 32–249（218 aa） Chain D 32–249（218 aa）	Not recorded	PO4 PHOSPHATE ION × 7 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；295 K；0.1 M HEPES pH 7.3, 1.4 M sodium potassium phosphate, 24% glycerol cryoprotectant	Resolution 3.20 Å R-free 0.277
6MOI Dimeric DARPin C_angle_R5 complex with EpoR Deposited 2018-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 32–249（218 aa）	Not recorded	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 20 MG MAGNESIUM ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.3 M magnesium sulfate, 0.1 M bis-tris propane pH 7, 22.5% PurePEGs cocktail (Anatrace), 30% ethylene glycol cryoprotectant	Resolution 2.06 Å R-free 0.251
6MOJ Dimeric DARPin A_angle_R5 complex with EpoR Deposited 2018-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 32–249（218 aa）	Not recorded	TAR D(-)-TARTARIC ACID × 6 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M sodium potassium tartrate, 0.1 M bis-tris propane pH 8.5, 20% PEG 3350, 30% glycerol as cryoprotectant	Resolution 2.43 Å R-free 0.250
6MOK Dimeric DARPin A_distance_R7 complex with EpoR Deposited 2018-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 32–249（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350	Resolution 5.10 Å R-free 0.299
6MOL Monoextended DARPin M_R12 complex with EpoR Deposited 2018-10-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 32–249（218 aa） Chain C 32–249（218 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；Seeded from 0.2 M NaCl, 0.1 M CAPS pH 10.5, 20% PEG 8000 into 0.2 M ammonium tartrate and 20% PEG 3350, with 10% glycerol, 10% ethylene glycol as cryoprotectant	Resolution 3.16 Å R-free 0.260
8VUI Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin receptor Deposited 2024-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 25–250（226 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 4 CL CHLORIDE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CIT CITRIC ACID × 1 NH4 AMMONIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；298 K；0.2 M Ammonium Citrate dibasic, 20% PEG2000 monomethyl ether, pH 5.2	Resolution 2.10 Å R-free 0.240
8VVM Structure of FabS1CE1-EPR1-1 in complex with the erythropoietin receptor Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 25–250（226 aa）	Mutation：residues 22-250	PEG DI(HYDROXYETHYL)ETHER × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；0.1 M MMT buffer pH 5.0, 25% PEG1500	Resolution 2.90 Å R-free 0.273
8VVO Structure of FabS1CE2-EPR1-1 in complex with the erythropoietin receptor Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 25–250（226 aa）	Mutation：residues 22-250	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1 M MMT buffer pH 6.0, 25% PEG1500	Resolution 3.09 Å R-free 0.289

20 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EPOR_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 6–223； UniProt 32–249 Author chain F； PDBConstruct 6–223； UniProt 32–249 Author chain I； PDBConstruct 6–223； UniProt 32–249 Author chain L； PDBConstruct 6–223； UniProt 32–249

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	4y5x
Deposition date deposition_date	2015-02-12
Structure title title	Diabody 305 complex with EpoR
Keywords keywords	diabody complex, receptor, protein binding-immune system complex; protein binding/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	63.23 Å
Radius of gyration Rg (electron density) rg_electron	65.17 Å
Forward intensity I(0) i0	522170000.00
Molecular weight molecular_weight	188660.0 kDa
Excluded volume excluded_volume	235020 Å³
Envelope volume envelope_volume	363500 Å³
Hydration-shell volume shell_volume	53911 Å³
Envelope diameter envelope_diameter	221.3 Å
Shell Rg shell_rg	50.51 Å
Envelope Rg envelope_rg	64.50 Å
Shape Rg shape_rg	65.16 Å
Total Rg total_rg	64.78 Å
Total atoms total_atoms	13306
Residues n_residues	1762
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	205.9 Å
Rg (real space) rg_real	64.77 Å
Rg uncertainty (real space) rg_real_error	2.29 Å
I(0) (real space) i0_real	5.2210e+08
I(0) uncertainty (real space) i0_real_error	1.0920e+07
Rg (reciprocal space) rg_reciprocal	61.82 Å
I(0) (reciprocal space) i0_reciprocal	519500000.0000
Solution quality estimate total_estimate	0.6666
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.0 Å
Skewness Skewness skewness	0.581
Kurtosis Kurtosis kurtosis	-0.604
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	14890000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.424; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.384; Smooth: 0.012

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	diabody 310 VL domain
Molecular weight formula_weight	14222.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	13334

HSAFAGSEVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCVKDRVAVAGKGSYYFDSWGRGTTVTVSSGGGGS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	diabody 310 VH domain
Molecular weight formula_weight	11912.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

QSVLTQPPSVSEAPGQRVTIACSGSSSNIGNNAVSWYQQLPGKAPTLLIYYDNLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNDWVFGGGTKVTVLAAAGGG

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Erythropoietin receptor
Molecular weight formula_weight	25129.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

FAGSADPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGQYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLDKEKAAA

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	Trichoplusia ni

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 5 Entity 5 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	28

▼

7. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d4y5xa_
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	d4y5xb1
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	d4y5xb2
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	d4y5xc1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d4y5xc2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d4y5xd_
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	d4y5xe1
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	d4y5xe2
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	d4y5xf1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d4y5xf2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d4y5xg_
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	d4y5xh1
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	d4y5xh2
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	d4y5xi1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d4y5xi2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d4y5xj_
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	d4y5xk1
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	d4y5xk2
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	d4y5xl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d4y5xl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

CATH v4.4 (16 domains)

Domain ID domain_id	4y5xA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xI01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xI02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4y5xL02
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	239.540 Å
Unit-cell length b length_b	239.540 Å
Unit-cell length c length_c	132.569 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	24.940 Å
R factor r_factor	0.2035
R_work r_work	0.2010
R_free r_free	0.2406

Diabody 305 complex with EpoR

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

diabody 310 VH domain

State in the Current Structure

Other States of the Same Protein in the Database

Erythropoietin receptor

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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (20 domains)

CATH v4.4 (16 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/y5/4y5x/4y5x.fit
pddf	/app/data/pr_computation/y5/4y5x/4y5x.pr.out
profile	/app/data/saxs_computation/y5/4y5x/4y5x.dat