1f8z

NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR

Method: SOLUTION NMR D_max: 31.1 Å Quality: GOOD

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

LOW-DENSITY LIPOPROTEIN RECEPTOR

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 234–272	Fragment：SIXTH LIGAND-BINDING MODULE	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

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 1F8Z	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 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 experimental conditions	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 ligand/ion Different experimental conditions	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
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 ligand/ion Different experimental conditions	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 ligand/ion Different experimental conditions	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 ligand/ion Different experimental conditions	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 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 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 ligand/ion Different experimental conditions	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 ligand/ion Different experimental conditions	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 ligand/ion Different experimental conditions	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 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 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 oligomeric state Different experimental conditions	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 ligand/ion Different experimental conditions	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 mutation/modification Different oligomeric state Different experimental conditions	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 experimental conditions	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 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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
9BDT Apolipoprotein B 100 bound to LDL receptor and legobody Deposited 2024-04-12	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 × 7 PDB declaration: heptameric	Chain I 1–860（860 aa） Chain R 1–860（860 aa）	Not recorded	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
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–39； UniProt 234–272

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1f8z
Deposition date deposition_date	2000-07-05
Structure title title	NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR
Keywords keywords	LDL receptor, ligand-binding domain, calcium-binding, familial hypercholesterolemia, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	8.97 Å
Radius of gyration Rg (electron density) rg_electron	9.24 Å
Forward intensity I(0) i0	166578000.00
Molecular weight molecular_weight	88115.0 kDa
Excluded volume excluded_volume	101520 Å³
Envelope volume envelope_volume	8377 Å³
Hydration-shell volume shell_volume	7140 Å³
Envelope diameter envelope_diameter	35.7 Å
Shell Rg shell_rg	15.65 Å
Envelope Rg envelope_rg	10.97 Å
Shape Rg shape_rg	9.24 Å
Total Rg total_rg	9.37 Å
Total atoms total_atoms	11040
Residues n_residues	780
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	31.1 Å
Rg (real space) rg_real	8.94 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.6660e+08
I(0) uncertainty (real space) i0_real_error	1.7870e+06
Rg (reciprocal space) rg_reciprocal	8.94 Å
I(0) (reciprocal space) i0_reciprocal	166600000.0000
Solution quality estimate total_estimate	0.8732
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	11.4 Å
Skewness Skewness skewness	0.182
Kurtosis Kurtosis kurtosis	-0.313
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17960.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1f8za_
Class class	g — Small proteins
Fold Fold fold	g.12 — LDL receptor-like module
Superfamily Superfamily superfamily	g.12.1 — LDL receptor-like module
Family Family family	g.12.1.1 — LDL receptor-like module

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	LOW-DENSITY LIPOPROTEIN RECEPTOR
Molecular weight formula_weight	4392.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11040

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR

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

LOW-DENSITY LIPOPROTEIN RECEPTOR

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/f8/1f8z/1f8z.fit
pddf	/app/data/pr_computation/f8/1f8z/1f8z.pr.out
profile	/app/data/saxs_computation/f8/1f8z/1f8z.dat