1ndg

Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme

Method: X-RAY DIFFRACTION Dmax: 99.8 Å Quality: GOOD

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

antibody kappa light chain

Mus musculus

UniProt P01837

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 A; UniProt 1–106 Fragment:light chain immunoglobulin gamma 1 chain × 1 (P01865) Lysozyme C × 1 (P00698) ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 1.90 Å R-free 0.249

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.

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

View Construct and Data Evidence
UniProt name KAC_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–214; UniProt 1–106

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 (P01837) Lysozyme C × 1 (P00698) ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 1.90 Å R-free 0.249

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 Mutation:R61A antibody kappa light chain × 1 (P01837) immunoglobulin gamma 1 chain × 1 (P01865) ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 1.90 Å R-free 0.249

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 1ndg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ndg
Deposition date deposition_date2002-12-09
Structure title titleCrystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme
Keywords keywordsantibody; lysozyme; mutant; HyHEL-8, 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_guinier29.45
Radius of gyration Rg (electron density) rg_electron28.82
Forward intensity I(0) i062673500.00
Molecular weight molecular_weight60247.0 kDa
Excluded volume excluded_volume74436 ų
Envelope volume envelope_volume93234 ų
Hydration-shell volume shell_volume28701 ų
Envelope diameter envelope_diameter101.3
Shell Rg shell_rg34.48
Envelope Rg envelope_rg28.59
Shape Rg shape_rg28.76
Total Rg total_rg29.50
Total atoms total_atoms4235
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 dmax99.8
Rg (real space) rg_real29.64
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real6.2670e+07
I(0) uncertainty (real space) i0_real_error1.0050e+06
Rg (reciprocal space) rg_reciprocal29.57
I(0) (reciprocal space) i0_reciprocal62670000.0000
Solution quality estimate total_estimate0.8647
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.6
Skewness Skewness skewness0.503
Kurtosis Kurtosis kurtosis-0.347
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8698000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.882; Smooth: 0.944

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1ndga1
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_idd1ndga2
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_idd1ndga3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1ndgb1
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_idd1ndgb2
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_idd1ndgc_
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_id1ndgA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ndgA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ndgB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ndgB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ndgC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)