← Back to search
1pn5

NMR structure of the NALP1 Pyrin domain (PYD)

Method: SOLUTION NMR Dmax: 50.9 Å Quality: REASONABLE
▼

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

NACHT-, LRR- and PYD-containing protein 2

Homo sapiens

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 Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 228–282 Fragment：Pyrin domain (PYD) No other associated polymer 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

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 1PN5 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 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 experimental conditions 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 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 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 experimental conditions 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 experimental conditions 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 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 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 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
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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental conditions 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 experimental method Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 conditions 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 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 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 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 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 method 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 experimental conditions 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 experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different experimental method Different experimental conditions 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 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 × 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 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 × 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 experimental conditions 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
9BDT Apolipoprotein B 100 bound to LDL receptor and legobody Deposited 2024-04-12 Different construct 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 B 295–352（58 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
9CHT Human E3 ligase E6AP in complex with HPV16-E6 and p53 Deposited 2024-07-02 Different construct Different oligomeric state Different experimental method Different experimental conditions 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 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 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 method 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 experimental method 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 experimental method 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 construct Different oligomeric state Different experimental method Different experimental conditions 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 1
Chains and sequence ranges Author chain A； PDBConstruct 2–56； UniProt 228–282

NACHT-, LRR- and PYD-containing protein 2

Homo sapiens

UniProt Q9C000

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 Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–93 Fragment：Pyrin domain (PYD) No other associated polymer 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

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 1PN5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3KAT Crystal Structure of the CARD domain of the human NLRP1 protein, Northeast Structural Genomics Consortium Target HR3486E Deposited 2009-10-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1371–1467（97 aa） Fragment：CARD domain
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 7.5；291 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 18% PEG3350 and 150 mM sodium formate., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.260
3KAT Crystal Structure of the CARD domain of the human NLRP1 protein, Northeast Structural Genomics Consortium Target HR3486E Deposited 2009-10-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1371–1467（97 aa） Fragment：CARD domain
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 7.5；291 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 18% PEG3350 and 150 mM sodium formate., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.260
4IFP X-ray Crystal Structure of Human NLRP1 CARD Domain Deposited 2012-12-14 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 1335–1418（84 aa） Fragment：NLRP1-CARD
Not recorded MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；1.4 M Malonate, 100 mM HEPES 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.99 Å R-free 0.208
4IFP X-ray Crystal Structure of Human NLRP1 CARD Domain Deposited 2012-12-14 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 1335–1418（84 aa） Fragment：NLRP1-CARD
Not recorded MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；1.4 M Malonate, 100 mM HEPES 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.99 Å R-free 0.208
4IFP X-ray Crystal Structure of Human NLRP1 CARD Domain Deposited 2012-12-14 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 1335–1418（84 aa） Fragment：NLRP1-CARD
Not recorded MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；1.4 M Malonate, 100 mM HEPES 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.99 Å R-free 0.208
4IM6 LRR domain from human NLRP1 Deposited 2013-01-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 791–990（200 aa） Fragment：LRR domain (UNP Residues 791-990)
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 8；293 K；0.1 M Tris pH 8.0, 0.02 M MgCl2, 25 % (w/v) PAA 5100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.183
4IM6 LRR domain from human NLRP1 Deposited 2013-01-02 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 × 2 PDB declaration: dimeric
Chain A 791–990（200 aa） Fragment：LRR domain (UNP Residues 791-990)
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris pH 8.0, 0.02 M MgCl2, 25 % (w/v) PAA 5100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.183
5Y3S Crystal structure of human NLRP1 leucine rich repeat domain Deposited 2017-07-30 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 790–990（201 aa） Fragment：UNP residues 790-990
Not recorded PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4
Resolution 2.45 Å R-free 0.259
5Y3S Crystal structure of human NLRP1 leucine rich repeat domain Deposited 2017-07-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 790–990（201 aa） Fragment：UNP residues 790-990
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4
Resolution 2.45 Å R-free 0.259
5Y3S Crystal structure of human NLRP1 leucine rich repeat domain Deposited 2017-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 790–990（201 aa） Fragment：UNP residues 790-990
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4
Resolution 2.45 Å R-free 0.259
5Y3S Crystal structure of human NLRP1 leucine rich repeat domain Deposited 2017-07-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 790–990（201 aa） Fragment：UNP residues 790-990
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4
Resolution 2.45 Å R-free 0.259
6K7V Structure of NLRP1 CARD filament Deposited 2019-06-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 1379–1466（88 aa）
Chain B 1379–1466（88 aa）
Chain C 1379–1466（88 aa）
Chain D 1379–1466（88 aa）
Chain E 1379–1466（88 aa）
Chain F 1379–1466（88 aa）
Chain G 1379–1466（88 aa）
Chain H 1379–1466（88 aa）
Chain I 1379–1466（88 aa）
Chain J 1379–1466（88 aa）
Chain K 1379–1466（88 aa）
Chain L 1379–1466（88 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å R-free 0.285
6X6A Cryo-EM structure of NLRP1-DPP9 complex Deposited 2020-05-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1212（1212 aa）
Chain C 1213–1473（261 aa）
Chain E 1–1212（1212 aa）
Chain F 1213–1473（261 aa）
Chain G 1213–1473（261 aa）
Chain I 1213–1473（261 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris pH 7.5, 150 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6X6C Cryo-EM structure of NLRP1-DPP9-VbP complex Deposited 2020-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–1473（1473 aa）
Chain F 1–1473（1473 aa）
Not recorded GK2 [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris pH 7.5, 150 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XKK Cryo-EM structure of the NLRP1-CARD filament Deposited 2020-06-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 44 PDB declaration: 44-meric
Chain A 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain B 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain C 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain D 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain E 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain F 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain G 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain H 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain I 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain J 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain K 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain L 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain M 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain N 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain O 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain P 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain Q 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain R 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain S 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain T 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain U 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain V 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain a 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain b 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain c 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain d 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain e 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain f 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain g 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain h 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain i 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain j 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain k 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain l 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain m 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain n 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain o 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain p 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain q 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain r 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain s 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain t 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain u 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Chain v 1305–1399（95 aa） Fragment：CARD domain (UNP residues 1305-1399)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
7WGE Human NLRP1 complexed with thioredoxin Deposited 2021-12-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 95–994（900 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8ZGD The Crystal Structure of the NLRP1_LRR domain from Biortus. Deposited 2024-05-09 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 791–990（200 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20mM MgCl2, 0.1M Tris pH 8.0, 19% polyacrylic acid 5100
Resolution 2.05 Å R-free 0.221
9BJ9 Human CRL-2 ZYG11B binding to human NLRP1 Gly/N degron Deposited 2024-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 131–139（9 aa） Fragment：residues 131-139 (Uniprot numbering)
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å

11 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NAL1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 59–151； UniProt 1–93

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 1pn5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pn5
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1pn5
Deposition date deposition_date2003-06-12
Structure title titleNMR structure of the NALP1 Pyrin domain (PYD)
Keywords keywords5 ALPHA-HELIX BUNDLE, APOPTOSIS; APOPTOSIS
Experimental Method methodSOLUTION NMR
▼

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

Radius of gyration Rg (Guinier) rg_guinier13.84 Å
Radius of gyration Rg (electron density) rg_electron13.13 Å
Forward intensity I(0) i0629460000.00
Molecular weight molecular_weight204470.0 kDa
Excluded volume excluded_volume252580 ų
Envelope volume envelope_volume32713 ų
Hydration-shell volume shell_volume16432 ų
Envelope diameter envelope_diameter56.8 Å
Shell Rg shell_rg22.82 Å
Envelope Rg envelope_rg17.12 Å
Shape Rg shape_rg13.10 Å
Total Rg total_rg13.47 Å
Total atoms total_atoms28220
Residues n_residues1860
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax50.9 Å
Rg (real space) rg_real13.79 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real6.2950e+08
I(0) uncertainty (real space) i0_real_error7.7960e+06
Rg (reciprocal space) rg_reciprocal13.80 Å
I(0) (reciprocal space) i0_reciprocal629500000.0000
Solution quality estimate total_estimate0.7186
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.0 Å
Skewness Skewness skewness0.309
Kurtosis Kurtosis kurtosis0.126
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha541800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.456; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1pn5a1
Class classa — All alpha proteins
Fold Fold folda.77 — DEATH domain
Superfamily Superfamily superfamilya.77.1 — DEATH domain
Family Family familya.77.1.5 — Pyrin domain, PYD

CATH v4.4 (1 domains)

Domain ID domain_id1pn5A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology533 — Death Domain, Fas
Homologous superfamily homologous superfamily10 — Death Domain, Fas
▶

8. Citations (1)

▶

9. Files and Curves (10)