1nbz

Crystal Structure of HyHEL-63 complexed with HEL mutant K97A

Method: X-RAY DIFFRACTION Dmax: 99.3 Å Quality: GOOD

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

immunoglobulin gamma 1 chain

Mus musculus

UniProt P01865

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–96 Not recorded antibody kappa light chain × 1 Lysozyme C × 1 (P00698) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.60, VAPOR DIFFUSION, HANGING DROP Resolution 1.85 Å R-free 0.229

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.

31 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GCAM_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 115–210; UniProt 1–96

Lysozyme C

Gallus gallus

UniProt P00698

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 19–147 Not recorded antibody kappa light chain × 1 immunoglobulin gamma 1 chain × 1 (P01865) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.60, VAPOR DIFFUSION, HANGING DROP Resolution 1.85 Å R-free 0.229

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.

1320 other PDB entries and 1450 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–129; UniProt 19–147

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 1nbz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1nbz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1nbz
Deposition date deposition_date2002-12-04
Structure title titleCrystal Structure of HyHEL-63 complexed with HEL mutant K97A
Keywords keywordsantibody, lysozyme, mutant, IMMUNE SYSTEM-HYDROLASE COMPLEX; IMMUNE SYSTEM/HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.64
Radius of gyration Rg (electron density) rg_electron29.03
Forward intensity I(0) i063677300.00
Molecular weight molecular_weight59968.0 kDa
Excluded volume excluded_volume73728 ų
Envelope volume envelope_volume94001 ų
Hydration-shell volume shell_volume28666 ų
Envelope diameter envelope_diameter101.7
Shell Rg shell_rg34.65
Envelope Rg envelope_rg28.84
Shape Rg shape_rg28.98
Total Rg total_rg29.70
Total atoms total_atoms4215
Residues n_residues553
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 dmax99.3
Rg (real space) rg_real29.84
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real6.3680e+07
I(0) uncertainty (real space) i0_real_error9.8010e+05
Rg (reciprocal space) rg_reciprocal29.76
I(0) (reciprocal space) i0_reciprocal63670000.0000
Solution quality estimate total_estimate0.8637
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0
Skewness Skewness skewness0.501
Kurtosis Kurtosis kurtosis-0.360
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8092000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.868; Smooth: 0.891

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1nbza1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1nbza2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1nbza3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1nbzb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1nbzb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1nbzc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.2 — C-type lysozyme

CATH v4.4 (5 domains)

Domain ID domain_id1nbzA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1nbzA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1nbzB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1nbzB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1nbzC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)