4im6

LRR domain from human NLRP1

Method: X-RAY DIFFRACTION Dmax: 65.5 Å Quality: GOOD

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

NACHT, LRR and PYD domains-containing protein 1

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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 791–990 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 791–990 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

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.

11 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NALP1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 7–206; UniProt 791–990

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 4im6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4im6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4im6
Deposition date deposition_date2013-01-02
Structure title titleLRR domain from human NLRP1
Keywords keywordsLRR domain, Ligand recognition, Muramyl dipeptide, Structural Protein; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.34
Radius of gyration Rg (electron density) rg_electron17.43
Forward intensity I(0) i09358970.00
Molecular weight molecular_weight22215.0 kDa
Excluded volume excluded_volume27732 ų
Envelope volume envelope_volume32019 ų
Hydration-shell volume shell_volume15883 ų
Envelope diameter envelope_diameter64.4
Shell Rg shell_rg23.10
Envelope Rg envelope_rg17.75
Shape Rg shape_rg17.45
Total Rg total_rg18.26
Total atoms total_atoms1549
Residues n_residues197
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax65.5
Rg (real space) rg_real18.35
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real9.3590e+06
I(0) uncertainty (real space) i0_real_error1.1200e+05
Rg (reciprocal space) rg_reciprocal18.35
I(0) (reciprocal space) i0_reciprocal9359000.0000
Solution quality estimate total_estimate0.8301
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.2
Skewness Skewness skewness0.429
Kurtosis Kurtosis kurtosis-0.071
Angular range angular_range— – 0.4350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1760000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.602; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4im6A00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor

8. Citations (1)

9. Files and Curves (10)