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9bdt

Apolipoprotein B 100 bound to LDL receptor and legobody

Method: ELECTRON MICROSCOPY Dmax: 342.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Apolipoprotein B-100

OrganismNot specified

UniProt P04114

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count Chain A； UniProt 1–4563 Not recorded Legobody 8D3 Fab Heavy Chain × 1 Legobody 8D3 Fab Light Chain × 1 Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G × 1 （C3SHQ8,P99134,P06654） Low-density lipoprotein receptor × 2 （P01130） ApoB100 nanobody 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 5.40 Å

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 9BDT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9BD1 beta/alpha1 region of ApoB 100 Deposited 2024-04-10 Different oligomeric state Different ligand/ion Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
9BD8 ApoB 100 beta barrel bound to LDLR beta propeller Deposited 2024-04-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
9BDE Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor Deposited 2024-04-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
9E9R The Structure of ApoB100 from Human Low-Density Lipoprotein Deposited 2024-11-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4563（4563 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
9EA7 The Structure of ApoB100 from Human Low-Density Lipoprotein Deposited 2024-11-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4563（4563 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
9EAG The Structure of ApoB100 from Human Low-Density Lipoprotein Deposited 2024-11-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4563（4563 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APOB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–4563； UniProt 1–4563

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Escherichia coli

UniProt C3SHQ8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count Chain B； UniProt 27–384 Not recorded Apolipoprotein B-100 × 1 （P04114） Legobody 8D3 Fab Heavy Chain × 1 Legobody 8D3 Fab Light Chain × 1 Low-density lipoprotein receptor × 2 （P01130） ApoB100 nanobody 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 5.40 Å

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 9BDT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6USM Structure of nuclease domain of human parvovirus B19 non-structural protein 1 in complex with zinc Deposited 2019-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–392（366 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.2 M LiSo4 and sodium acetate tri-hydrate buffer of pH4.6
Resolution 3.37 Å
6WH0 Crystal structure of HyBcl-2-4 with HyBax BH3 Deposited 2020-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–392（366 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2M Magnesium chloride hexahydrate, 0.1 Bis Tris pH 5.5, 25% PEG 3350
Resolution 1.99 Å R-free 0.268
7JHG Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody Deposited 2020-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 26–392（367 aa）
Not recorded TAK 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7JHH Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody Deposited 2020-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 26–392（367 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–392（366 aa） Fragment：KER domain, residues 136-225
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300
Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–392（366 aa） Fragment：KER domain, residues 136-225
Not recorded PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300
Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 27–392（366 aa） Fragment：KER domain, residues 136-225
Not recorded PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300
Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 27–392（366 aa） Fragment：KER domain, residues 136-225
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300
Resolution 2.81 Å R-free 0.282
8E0P Crystal structure of mouse APCDD1 in fusion with engineered MBP Deposited 2022-08-09 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–392（364 aa）
Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PLM PALMITIC ACID × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol
Resolution 2.33 Å R-free 0.239
8E0P Crystal structure of mouse APCDD1 in fusion with engineered MBP Deposited 2022-08-09 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain B 29–392（364 aa）
Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol
Resolution 2.33 Å R-free 0.239
8E0P Crystal structure of mouse APCDD1 in fusion with engineered MBP Deposited 2022-08-09 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain C 29–392（364 aa）
Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PLM PALMITIC ACID × 1 GOL GLYCEROL × 1 DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol
Resolution 2.33 Å R-free 0.239
8E0P Crystal structure of mouse APCDD1 in fusion with engineered MBP Deposited 2022-08-09 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain D 29–392（364 aa）
Mutation：D84A, K85A, E174A, N175A, A217H, K221H, K241A, A314V, I319V, E361A, K364A, D365A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol
Resolution 2.33 Å R-free 0.239
8IIY Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide Deposited 2023-02-24 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 × 3 PDB declaration: trimeric
Chain A 27–392（366 aa）
Mutation：D108A, K109A, E198A, N199A, K265A GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
Resolution 2.15 Å R-free 0.247
8IIZ Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide Deposited 2023-02-24 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 × 3 PDB declaration: trimeric
Chain A 27–392（366 aa）
Mutation：D108A, K109A, E198A, N199A, K265A GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
Resolution 2.10 Å R-free 0.301
8SQB The cryo-EM structure of the EcBAM/EspP(beta7-12) complex Deposited 2023-05-04 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 26–392（367 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9B83 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from human GLI1 gene Deposited 2024-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 27–392（366 aa）
Chain B 27–392（366 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
9B84 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene Deposited 2024-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 27–392（366 aa）
Chain B 27–392（366 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B89 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene in the pre-editing state Deposited 2024-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 27–392（366 aa）
Chain B 27–392（366 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 27–384（358 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
9IVP 24-mer DARPin-apoferritin scaffold in complex with the maltose binding protein Deposited 2024-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain AA 27–392（366 aa）
Chain B 27–392（366 aa）
Chain CA 27–392（366 aa）
Chain D 27–392（366 aa）
Chain EA 27–392（366 aa）
Chain F 27–392（366 aa）
Chain GA 27–392（366 aa）
Chain H 27–392（366 aa）
Chain IA 27–392（366 aa）
Chain J 27–392（366 aa）
Chain KA 27–392（366 aa）
Chain L 27–392（366 aa）
Chain MA 27–392（366 aa）
Chain N 27–392（366 aa）
Chain OA 27–392（366 aa）
Chain P 27–392（366 aa）
Chain QA 27–392（366 aa）
Chain R 27–392（366 aa）
Chain SA 27–392（366 aa）
Chain T 27–392（366 aa）
Chain UA 27–392（366 aa）
Chain W 27–392（366 aa）
Chain WA 27–392（366 aa）
Chain Y 27–392（366 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9ZVM Dimer structure of Thlaspi arvense plastid biotin carboxylase Deposited 2025-12-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 27–392（366 aa）
Chain D 27–392（366 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50mM HEPES pH 8.0, 4mM MgCl2, 5% glycerol, 0.5mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å

15 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C3SHQ8_ECOLX
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 2–359； UniProt 27–384

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Escherichia coli

UniProt P06654

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count Chain B； UniProt 295–352 Not recorded Apolipoprotein B-100 × 1 （P04114） Legobody 8D3 Fab Heavy Chain × 1 Legobody 8D3 Fab Light Chain × 1 Low-density lipoprotein receptor × 2 （P01130） ApoB100 nanobody 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 5.40 Å

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 9BDT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EM7 HELIX VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G Deposited 2000-03-16 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 189–244（56 aa） Fragment：B1 DOMAIN
Mutation：A24E, K28R, Q32E, N35K, D36K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；100 mM sodium acetate, 30% polyethylene glycol momomethyl Ether 2000, 200 mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.267
1GB1 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G Deposited 1991-05-15 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 228–282（55 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1IGC IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS Deposited 1994-08-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 293–352（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1IGD THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G: AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB Deposited 1994-08-05 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 293–352（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.10 Å
1LE3 NMR Structure of Tryptophan Zipper 4: A Stable Beta-Hairpin Peptide Based on the C-terminal Hairpin of the B1 Domain of Protein G Deposited 2002-04-09 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 267–282（16 aa） Fragment：C-terminal hairpin of the B1 domain of Protein G
Mutation：Y45W/F52W/V54W Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 2mM trpzip4 | 92% H2O, 8% D2O, pH 6.0, 0.1mM DSS
Resolution not provided
1MPE Ensemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain B 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain C 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain D 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.45；313 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate, 0.02% sodium azide；Pressure 1
NMR sample composition 3.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide | 90% H2O/10% D2O
NMR sample composition 2.89 mM (in monomer) U-15N, 50 mM sodium phosphate buffer, 0.02% sodium azide | 90% H2O/10% D2O
NMR sample composition 3.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide | 100% D2O
NMR sample composition 1.4 mM (in monomer) 1:1 mixture unlabelled:U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide | 100% D2O
Resolution not provided
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain B 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain C 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain D 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.283
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain F 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain G 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain H 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.283
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain J 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain K 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain L 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.283
1PGA TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON WITH NMR Deposited 1993-11-23 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 228–282（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.07 Å
1PGB TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR Deposited 1993-11-23 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 228–282（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.92 Å
1PGX THE 1.66 ANGSTROMS X-RAY STRUCTURE OF THE B2 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON TO THE NMR STRUCTURE OF THE B1 DOMAIN Deposited 1992-04-03 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 284–366（83 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.66 Å
1PN5 NMR structure of the NALP1 Pyrin domain (PYD) Deposited 2003-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa） Fragment：Pyrin domain (PYD)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Pressure 1
NMR sample composition 1mM NALP1 PYD U-15N,13C; 50mM Na / PO4 - Buffer; 50mM NaCl; 1mM CHAPS; 20mM DTT (D10); 0.02% NaN3; 0.1mM EDTA; protease inhibitor cocktail (Complete, Roche); 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided
1Q10 Ensemble of 40 Structures of the Dimeric Mutant of the B1 Domain of Streptococcal Protein G Deposited 2003-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 228–282（55 aa） Fragment：B1 Domain
Chain B 228–282（55 aa） Fragment：B1 Domain
Mutation：T228Q,L231V,F256V,Y259F,A260F Mutation：T228Q,L231V,F256V,Y259F,A260F No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate buffer；Pressure ambient
NMR sample composition 1.7mM (in monomer) U-15N,13C, 50mM phosphate buffer, 0.02% NaN3, 92.5% H2O, 7.5% D2O | 92.5% H2O, 7.5% D2O
NMR sample composition 0.85mM (in monomer) U-15N,13C, 0.85mM (in monomer) unlabeled, 50mM phosphate buffer (pH 5.5), 0.02 % NaN3, 92.5% H2O, 7.5% D2O | 92.5% H2O, 7.5% D2O
NMR sample composition 0.85mM (in monomer) U-15N,13C, 0.85mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 100% D2O | 100% D2O
NMR sample composition 1.7mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 92.5% H2O, 7.5% D2O | 92.5% H2O, 7.5% D2O
NMR sample composition 1.7mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 100% D2O | 100% D2O
Resolution not provided
2CWB Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin Deposited 2005-06-17 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–282（54 aa） Fragment：C-TERMINAL UBA DOMAIN,C-TERMINAL UBA DOMAIN
Mutation：I12A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient
NMR sample composition 1mM HGB1-UBA U-15N,13C; 20mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2DEN Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin Deposited 2006-02-14 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 × 2 PDB declaration: dimeric
Chain A 229–282（54 aa） Fragment：UBA domain,UBA domain
Mutation：I12A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 1mM HGB1-UBA | 20mM phosphate, 100mM NaCl, pH6.5
NMR sample composition 1mM Ubiquitin | 20mM phosphate, 100mM NaCl, pH6.5
Resolution not provided
2GB1 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G Deposited 1991-05-15 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 228–282（55 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2IGD ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ANGSTROM RESOLUTION Deposited 1997-04-30 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 293–352（60 aa） Fragment：IMMUNOGLOBULIN-BINDING DOMAIN III
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；CRYSTALS WERE GROWN BY HANGING DROP VAPOUR DIFFUSION FROM 24-26% PEG 4000, 10MM SODIUM ACETATE AT PH 4.8 AND 0.01% SODIUM AZIDE. CELL PARAMETERS ARE NOT THOSE DETERMINED EXPERIMENTALLY. THEY WERE ADJUSTED ON THE BASIS OF THE ENGH & HUBER DICTIONARY AT THE END OF REFINEMENT. THE EXPERIMENTAL ESTIMATES WERE KNOWN TO HAVE POTENTIAL ERRORS DUE TO INACCURACIES IN THE CRYSTAL-TO-DETECTOR AND WAVELENGTH CALIBRATION., vapor diffusion - hanging drop
Resolution 1.10 Å R-free 0.125
2IGH DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR Deposited 1992-08-26 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 292–352（61 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2J52 Solution Structure of GB1 domain Protein G and low and high pressure. Deposited 2006-09-11 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 228–282（55 aa） Fragment：RESIDUES 228-282
Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.4；287 K；Ionic strength (raw mmCIF value) 0.1；Pressure 30.0
NMR sample composition 90%WATER/10%D2O
Resolution not provided
2J53 Solution Structure of GB1 domain Protein G and low and high pressure. Deposited 2006-09-11 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 228–282（55 aa） Fragment：RESIDUES 228-282
Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.4；287 K；Ionic strength (raw mmCIF value) 0.1；Pressure 2000.0
NMR sample composition 90%WATER/10%D2O
Resolution not provided
2JU6 Solid-State Protein Structure Determination with Proton-Detected Triple Resonance 3D Magic-Angle Spinning NMR Spectroscopy Deposited 2007-08-15 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 X 228–282（55 aa）
Mutation：T2Q No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 5.5；281 K；Pressure ambient
NMR sample composition 5 mM [U-13C; U-15N; U-2H] GB1, 50 % isopropyl alcohol, 25 % (4R)-2-Methylpentane-2,4-diol, 50 mM sodium phosphate, Solid Slurry | Solid Slurry
Resolution not provided
2K0P Determination of a Protein Structure in the Solid State from NMR Chemical Shifts Deposited 2008-02-11 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 228–282（55 aa） Fragment：GB1
Mutation：T2Q No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions 278 K；Pressure 1
NMR sample composition 10 mg/mL [U-100% 13C; U-100% 15N] GB1, 0.5 v/v Methyl Pentane diol, 0.25 v/v Isopropanol | 0.5 v/v Methyl Pentane diol/0.25 v/v Isopropanol
Resolution not provided
2KBT Attachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method Deposited 2008-12-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa） Fragment：SH3 2 domain of Proto-oncogene vav,UNP residues 228-282 of Immunoglobulin G-binding protein G
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 20 mM MES-1, 2 mM DTT-2, 150 mM NaCl-3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LGI Atomic Resolution Protein Structures using NMR Chemical Shift Tensors Deposited 2011-07-26 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 229–282（54 aa） Fragment：2-1 repeat region residues 229-282
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 5.5；273 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 20 mg U-2-13C-glycerol; U-100% 15N GB1 | solid
Resolution not provided
2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 229–282（54 aa） Fragment：UNP P06654 residues 229-282, UNP Q9UNA4 residues 516-555
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
2N7J Sidechain chi1 distribution in B3 domain of protein G from extensive sets of residual dipolar couplings Deposited 2015-09-12 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 299–352（54 aa） Fragment：residues 299-352
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K, 100% D2O | 100% D2O
NMR sample composition 1.3 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K, 100% D2O | 100% D2O
NMR sample composition 1.3 mM [U-13C; U-15N; U-2H] GB3-K19A/V42E/D47K, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E, 100% D2O | 100% D2O
NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E, 100% D2O | 100% D2O
NMR sample composition 2.0 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3, 100% D2O | 100% D2O
NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K, 100% D2O | 100% D2O
NMR sample composition 2.5 mM [U-13C; U-15N; U-2H] wild-type GB3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6, 100% D2O | 100% D2O
NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E-CHis6, 100% D2O | 100% D2O
NMR sample composition 0.9 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E-CHis6, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2NMQ Simultaneous determination of protein structure and dynamics using rdcs Deposited 2006-10-23 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 298–352（55 aa） Fragment：protein GB3(residues 298-352)
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2RMM Solution structure of GB1 A34F mutant Deposited 2007-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 229–282（54 aa）
Chain B 229–282（54 aa）
Mutation：A34F Mutation：A34F No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 2.0mM [U-99% 13C; U-99% 15N] entity, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2RPV Solution Structure of GB1 with LBT probe Deposited 2008-10-28 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 227–282（56 aa） Fragment：L2GB
Mutation：E38C LA LANTHANUM (III) ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.8mM [U-99% 13C; U-99% 15N] L2GB, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26 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 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)
Not recorded FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.20 Å R-free 0.181
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)
Not recorded FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.20 Å R-free 0.181
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)
Chain B 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)
Not recorded FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.20 Å R-free 0.181
6CNE Selenomethionine variant (V29SeM) of protein GB1 Deposited 2018-03-08 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 229–282（54 aa）
Mutation：L5Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；283.15 K；47% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 Non-reducing conditions (no TCEP)
Resolution 1.20 Å R-free 0.198
6CNE Selenomethionine variant (V29SeM) of protein GB1 Deposited 2018-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 229–282（54 aa）
Mutation：L5Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；283.15 K；47% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 Non-reducing conditions (no TCEP)
Resolution 1.20 Å R-free 0.198
6L91 X-ray structure of synthetic GB1 domain with the mutation K10(DVA). Deposited 2019-11-07 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 227–282（56 aa）
Mutation：K10(DVA) Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1M NaCacodylate (pH 5.5), 20% PEG 4000
Resolution 1.84 Å R-free 0.186
6L9B X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11A Deposited 2019-11-08 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 227–282（56 aa）
Mutation：K10(DVA), T11A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.2M CaCl2, 0.1M sodium acetate (pH 4.6), 30% Isopropanol
Resolution 1.95 Å R-free 0.250
6L9D X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11S Deposited 2019-11-08 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 227–282（56 aa）
Mutation：K10DVA, T11S Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Sodium Cacodylate (pH 6), 20% PEG 4000
Resolution 1.73 Å R-free 0.243
6LJI X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V Deposited 2019-12-16 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 227–282（56 aa） Fragment：GB1 domain
Mutation：K10(DVA), T11V Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；20% PEG 4000, 0.1M MES pH 6.0
Resolution 1.84 Å R-free 0.328
6LJI X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V Deposited 2019-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 227–282（56 aa） Fragment：GB1 domain
Mutation：K10(DVA), T11V Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；20% PEG 4000, 0.1M MES pH 6.0
Resolution 1.84 Å R-free 0.328
6V9I cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) Deposited 2019-12-13 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 C 229–282（54 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20
Resolution 5.20 Å
7QTR GB1 in mammalian cells, 50 uM Deposited 2022-01-15 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 229–282（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；283 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 50 uM [U-13C; U-15N] B1 domain of streptococcal protein G (GB1), 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7QTS GB1 in mammalian cells, 10 uM Deposited 2022-01-15 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 229–282（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；283 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 10 uM [U-13C; U-15N] GB1, in-cell | in-cell
Resolution not provided
7RXC CryoEM structure of KDELR with Legobody Deposited 2021-08-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 295–352（58 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7RXD CryoEM structure of RBD domain of COVID-19 in complex with Legobody Deposited 2021-08-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 295–352（58 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8JXR Structure of nanobody-bound DRD1_LSD complex Deposited 2023-07-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 295–352（58 aa）
Mutation：E360Q,K363A,D364F,T367I,R368L 7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.57 Å
8JXS Structure of nanobody-bound DRD1_PF-6142 complex Deposited 2023-07-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 295–352（58 aa）
Mutation：E360Q,K363A,D364F,T367I,R368L,D404E,A405H V6X 4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8T0G Backbone Dialkylation in Peptide Hairpins: Natural Backbone Prototype Deposited 2023-06-01 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 267–282（16 aa）
Mutation：T13A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR sample composition 2 mM GB1 C-terminal Hairpin Mutant: Ala13 variant, 50 mM sodium phosphate, 0.2 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9CHT Human E3 ligase E6AP in complex with HPV16-E6 and p53 Deposited 2024-07-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 228–282（55 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 295–352（58 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
9G4T Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome Deposited 2024-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: monomeric
Chain A 229–282（54 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.51 Å
9JA5 Cryo-EM structure of Tdk1-Bdf1 complex Deposited 2024-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 228–282（55 aa）
Chain B 228–282（55 aa）
Chain C 228–282（55 aa）
Chain D 228–282（55 aa）
Chain E 228–282（55 aa）
Chain F 228–282（55 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 2.70 Å
9JA6 Cryo-EM structure of Tdk1 tetramer complex Deposited 2024-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 228–282（55 aa）
Chain B 228–282（55 aa）
Chain C 228–282（55 aa）
Chain D 228–282（55 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 4.40 Å
9W3K GPR151-Legobody complex Deposited 2025-07-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 295–352（58 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å

48 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPG1_STRSG
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 479–536； UniProt 295–352

Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Escherichia coli

UniProt P99134

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count Chain B； UniProt 43–151 Not recorded Apolipoprotein B-100 × 1 （P04114） Legobody 8D3 Fab Heavy Chain × 1 Legobody 8D3 Fab Light Chain × 1 Low-density lipoprotein receptor × 2 （P01130） ApoB100 nanobody 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 5.40 Å

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 9BDT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7RXC CryoEM structure of KDELR with Legobody Deposited 2021-08-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 43–151（109 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7RXD CryoEM structure of RBD domain of COVID-19 in complex with Legobody Deposited 2021-08-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 43–151（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 43–151（109 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
9QBJ Legobody dimer Deposited 2025-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain I 103–151（49 aa）
Chain J 103–151（49 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPA_STAAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 360–467； UniProt 43–151

Low-density lipoprotein receptor

Homo sapiens

UniProt P01130

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count Chain I； UniProt 1–860 Chain R； UniProt 1–860 Not recorded Apolipoprotein B-100 × 1 （P04114） Legobody 8D3 Fab Heavy Chain × 1 Legobody 8D3 Fab Light Chain × 1 Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G × 1 （C3SHQ8,P99134,P06654） ApoB100 nanobody 4 × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 5.40 Å

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 9BDT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AJJ LDL RECEPTOR LIGAND-BINDING MODULE 5, CALCIUM-COORDINATING Deposited 1997-05-04 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 196–232（37 aa） Fragment：LIGAND-BINDING DOMAIN, FIFTH REPEAT
Not recorded SO4 SULFATE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLIZED FROM 2.1 M AMMONIUM SULFATE, PH 5.0, 25% SUCROSE
Resolution 1.70 Å R-free 0.240
1D2J LDL RECEPTOR LIGAND-BINDING MODULE 6 Deposited 1999-09-23 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 233–272（40 aa） Fragment：LIGAND-BINDING DOMAIN, SIXTH REPEAT
Mutation：M243L CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR sample composition 1 MM LR6 U-15N; 10 MM CACL2
NMR sample composition 1 MM LR6 U-15N; 10 MM CACL2
NMR sample composition 1 MM LR6 UNLABELED; 10 MM CACL2
NMR sample composition 1 MM LR6 UNLABELED; 10 MM CACL2
Resolution not provided
1F5Y NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BINDING MODULES OF THE HUMAN LDL RECEPTOR Deposited 2000-06-18 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 22–104（83 aa） Fragment：LIGAND-BINDING MODULES 1-2
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 5.5；310 K；Ionic strength (raw mmCIF value) 0.045；Pressure atmospheric
NMR sample composition 1 mM LB1-2, 15 mM CaCl2, pH 5.5 | 95% H2O/5% D2O
NMR sample composition 1 mM LB1-2, 15 mM CaCl2, pH 5.5 | 99% D2O
Resolution not provided
1F8Z NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR Deposited 2000-07-05 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 234–272（39 aa） Fragment：SIXTH LIGAND-BINDING MODULE
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR sample composition 3 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate | 90% H2O/10% D2O
NMR sample composition 3 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate | 100% D2O
Resolution not provided
1HJ7 NMR study of a pair of LDL receptor Ca2+ binding epidermal growth factor-like domains, 20 structures Deposited 2001-01-09 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 314–393（80 aa） Fragment：CA2+ BINDING EPIDERMAL GROWTH FACTOR-LIKE DOMAIN PAIR, RESIDUES 293-372
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) SEE REFERENCES
NMR sample composition SEE REFERENCES
Resolution not provided
1HZ8 SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR Deposited 2001-01-23 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 314–395（82 aa） Fragment：EGF-AB CONCATEMER (RESIDUES 314-395)
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 5.5；310 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR measurement conditions pH 5.5；283 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR measurement conditions pH 5.5；295 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR sample composition 1mM EGF-AB, 20mM CaCl2 | 95% H2O/5% D2O
NMR sample composition 1mM EGF-AB, 20mM CaCl2 | 99% D2O
NMR sample composition 1mM 15N-EGF-AB, 20mM CaCl2 | 95% H2O/5% D2O
NMR sample composition 1.5mM EGF-A, 20mM CaCl2 | 99% D2O
NMR sample composition 1.5mM EGF-A, 20mM CaCl2 | 95% H2O/5% D2O
Resolution not provided
1I0U SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR Deposited 2001-01-29 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 314–395（82 aa） Fragment：EGF-AB CONCATEMER(RESIDUES 314-395)
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 5.5；310 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR measurement conditions pH 5.5；283 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR measurement conditions pH 5.5；295 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR sample composition 1mM EGF-AB, 20mM CaCl2 | 95% H2O/5% D2O
NMR sample composition 1mM EGF-AB, 20mM CaCl2 | 99% D2O
NMR sample composition 1mM 15N-EGF-AB, 20mM CaCl2 | 95% H2O/5% D2O
NMR sample composition 1.5mM EGF-A, 20mM CaCl2 | 99% D2O
NMR sample composition 1.5mM EGF-A, 20mM CaCl2 | 95% H2O/5% D2O
Resolution not provided
1IJQ Crystal Structure of the LDL Receptor YWTD-EGF Domain Pair Deposited 2001-04-27 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 398–713（316 aa） Fragment：YWTD-E3 DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG4000,2-propanol,HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.250
1IJQ Crystal Structure of the LDL Receptor YWTD-EGF Domain Pair Deposited 2001-04-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 398–713（316 aa） Fragment：YWTD-E3 DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG4000,2-propanol,HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.250
1LDL THREE-DIMENSIONAL STRUCTURE OF A CYSTEINE-RICH REPEAT FROM THE LOW-DENSITY LIPOPROTEIN RECEPTOR Deposited 1995-03-20 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 20–67（48 aa） Fragment：LIGAND-BINDING DOMAIN, FIRST REPEAT
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1LDR SECOND REPEAT OF THE LDL RECEPTOR LIGAND-BINDING DOMAIN Deposited 1995-08-17 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 55–104（50 aa） Fragment：LIGAND-BINDING DOMAIN, SECOND REPEAT
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1N7D Extracellular domain of the LDL receptor Deposited 2002-11-13 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–720（699 aa） Fragment：extracellular domain, RESIDUES 1-699
Mutation：N494Q, N636Q CA CALCIUM ION × 8 KEG 12-TUNGSTOPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；298 K；acetate buffer pH 5.3, 1,2-hexanediol, 0.5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.70 Å R-free 0.382
1XFE Solution structure of the LA7-EGFA pair from the LDL receptor Deposited 2004-09-14 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 272–353（82 aa） Fragment：sequence database residues 272-353: includes LDL-receptor class A 7 (residues 274-313), EGF-like 1 (314-353)
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 1:6 molar protein/CaCl2；Pressure ambient
NMR sample composition 0.3 mM LA7-EGFA U-15N,13C 2 mM CaCl2; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.5 mM LA7-EGFA U-15N 10 mM CaCl2; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.6 mMM LA7-EGFA U-15N, 10% 13C 4 mM CaCl2; 99% D2O | 99% D2O
NMR sample composition 1 mM LA7-EGFA 6 mM CaCl2; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2FCW Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP). Deposited 2005-12-12 Different construct Different mutation/modification 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 107–186（80 aa） Fragment：A Pair of Ligand-Binding Modules 3 and 4
Not recorded NA SODIUM ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；40% MPD, 100 mM HEPES, 75 mM NaCl, 1.25 mM CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.26 Å R-free 0.200
2FCW Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP). Deposited 2005-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 107–186（80 aa） Fragment：A Pair of Ligand-Binding Modules 3 and 4
Not recorded NA SODIUM ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 10 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；40% MPD, 100 mM HEPES, 75 mM NaCl, 1.25 mM CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.26 Å R-free 0.200
2KRI Structure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock Deposited 2009-12-18 Different construct Different mutation/modification 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 147–186（40 aa） Fragment：LDL-receptor class A 4 domain
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 25；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_2-1, 100 uM [U-100% 15N] entity_2-2, 300 uM [U-100% 15N] entity_2-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 600 uM [U-100% 13C; U-100% 15N] entity_1-4, 300 uM [U-100% 15N] entity_1-5, 515 uM [U-100% 15N] entity_1-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LGP Solution structure of LA45 from LDLR Deposited 2011-08-01 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 144–235（92 aa） Fragment：LDL-receptor class A 4 and A5 domain residues 144-235
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.45；306 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 0.02 % sodium azide, 20 mM [U-99% 2H] HEPES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 0.02 % sodium azide, 150 mM sodium chloride, 20 mM [U-99% 2H] HEPES, 100% D2O | 100% D2O
Resolution not provided
2M7P RXFP1 utilises hydrophobic moieties on a signalling surface of the LDLa module to mediate receptor activation Deposited 2013-04-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–68（3 aa）
Chain A 82–104（23 aa）
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] LDLA-1, 50 mM Immidazole-2, 10 mM CaCl2-3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MG9 Truncated EGF-A Deposited 2013-10-30 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 314–339（26 aa） Fragment：EGF-A domain, UNP RESIDUES 314-339
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 5.3；283 K；Pressure ambient
NMR sample composition 1 mM egfa-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2W2M WT PCSK9-DELTAC BOUND TO WT EGF-A OF LDLR Deposited 2008-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
Not recorded CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (V/V) 2-PROPANOL, 20% (W/V) PEG 4000
Resolution 2.40 Å R-free 0.254
2W2N WT PCSK9-deltaC bound to EGF-A H306Y mutant of LDLR Deposited 2008-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
Mutation：YES CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (W/V) PEG 8000, 8% (V/V) ETHYLENE GLYCOL.
Resolution 2.30 Å R-free 0.254
2W2O PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR Deposited 2008-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL
Resolution 2.62 Å R-free 0.263
2W2P PCSK9-deltaC D374A mutant bound to WT EGF-A of LDLR Deposited 2008-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL
Resolution 2.62 Å R-free 0.270
2W2Q PCSK9-deltaC D374H mutant bound to WT EGF-A of LDLR Deposited 2008-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL
Resolution 2.33 Å R-free 0.253
3BPS PCSK9:EGF-A complex Deposited 2007-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-like 1, EGF-like 2 domains, UNP residues 314-393
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；294 K；0.3M (NH4)H2PO4, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 4.80
Resolution 2.41 Å R-free 0.240
3GCW PCSK9:EGFA(H306Y) Deposited 2009-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa）
Mutation：H306Y CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；294 K；0.3M (NH4)H2PO4, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.70 Å R-free 0.278
3GCX PCSK9:EGFA (pH 7.4) Deposited 2009-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；294 K；0.3M (NH4)H2PO4, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.70 Å R-free 0.261
3M0C The X-ray Crystal Structure of PCSK9 in Complex with the LDL receptor Deposited 2010-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 4–788（785 aa） Fragment：LDLR
Not recorded CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；297 K；1.4 M Ammonium phosphate, 0.2M sodium chloride in 0.1M Imidazole buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 7.01 Å R-free 0.362
3SO6 Crystal structure of the LDL receptor tail in complex with autosomal recessive hypercholesterolemia PTB domain Deposited 2011-06-29 Different construct Different mutation/modification 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 Q 819–832（14 aa） Fragment：UNP residues 817-832
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES, 30% PEG6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.37 Å R-free 0.206
4NE9 PCSK9 in complex with LDLR peptide Deposited 2013-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 314–339（26 aa） Fragment：UNP residues 314-339
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；299 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Resolution 2.60 Å R-free 0.211
5OY9 VSV G CR3 Deposited 2017-09-08 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 × 2 PDB declaration: dimeric
Chain D 108–144（37 aa） Fragment：UNP residues 108-144
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% PEG 400, 50 mM Tris-HCl pH 8.5, 200 mM CaCl2, 0.2% dodecylmaltoside
Resolution 3.60 Å R-free 0.268
5OYL VSV G CR2 Deposited 2017-09-11 Different construct Different mutation/modification 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 D 65–106（42 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2 GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；29% PEG 3000, 100 mM Tris-HCl pH 8.5, 200 mM LiSO4
Resolution 2.25 Å R-free 0.224
9BD8 ApoB 100 beta barrel bound to LDLR beta propeller Deposited 2024-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–860（860 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
9BDE Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor Deposited 2024-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–860（860 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 66–860（795 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å

33 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LDLR_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain I； PDBConstruct 1–860； UniProt 1–860 Author chain R； PDBConstruct 1–860； UniProt 1–860

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 9bdt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9bdt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9bdt
Deposition date deposition_date2024-04-12
Structure title titleApolipoprotein B 100 bound to LDL receptor and legobody
Keywords keywordsLDL, ApoB100, LDL receptor, LIPID TRANSPORT; LIPID TRANSPORT
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier— Å
Radius of gyration Rg (electron density) rg_electron114.30 Å
Forward intensity I(0) i04200570000.00
Molecular weight molecular_weight552380.0 kDa
Excluded volume excluded_volume690960 ų
Envelope volume envelope_volume2387300 ų
Hydration-shell volume shell_volume193660 ų
Envelope diameter envelope_diameter341.3 Å
Shell Rg shell_rg106.40 Å
Envelope Rg envelope_rg95.24 Å
Shape Rg shape_rg114.30 Å
Total Rg total_rg114.20 Å
Total atoms total_atoms38899
Residues n_residues5048
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax342.6 Å
Rg (real space) rg_real116.90 Å
Rg uncertainty (real space) rg_real_error1.71 Å
I(0) (real space) i0_real4.1760e+09
I(0) uncertainty (real space) i0_real_error9.6840e+07
Rg (reciprocal space) rg_reciprocal111.10 Å
I(0) (reciprocal space) i0_reciprocal4138000000.0000
Solution quality estimate total_estimate0.8675
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary171.3 Å
Skewness Skewness skewness0.039
Kurtosis Kurtosis kurtosis-0.869
Angular range angular_range— – 0.0700 Å−1
Current regularization parameter α current_alpha1.3420
Highest regularization parameter α highest_alpha162800000.0000
Real-space data points n_real_points15
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 0.883; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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8. Citations (1)

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9. Files and Curves (10)