4i0c

The structure of the camelid antibody cAbHuL5 in complex with human lysozyme

Method: X-RAY DIFFRACTION Dmax: 135.0 Å Quality: REASONABLE

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

Lysozyme C

Homo sapiens

UniProt P61626

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 19–148 Not recorded cAbHuL5 antibody × 1 CL CHLORIDE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;4.8 M NaCl, 0.1 M HEPES pH 7, 3% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.95 Å R-free 0.219
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 19–148 Not recorded cAbHuL5 antibody × 1 CL CHLORIDE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;4.8 M NaCl, 0.1 M HEPES pH 7, 3% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.95 Å R-free 0.219

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.

201 other PDB entries and 218 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–130; UniProt 19–148 Author chain B; PDBConstruct 1–130; UniProt 19–148

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 4i0c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4i0c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4i0c
Deposition date deposition_date2012-11-16
Structure title titleThe structure of the camelid antibody cAbHuL5 in complex with human lysozyme
Keywords keywordsbeta-barrel, alpha-beta protein, immune recognition, glycosidase, 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_guinier43.52
Radius of gyration Rg (electron density) rg_electron43.78
Forward intensity I(0) i053960900.00
Molecular weight molecular_weight56536.0 kDa
Excluded volume excluded_volume69194 ų
Envelope volume envelope_volume100480 ų
Hydration-shell volume shell_volume19883 ų
Envelope diameter envelope_diameter141.9
Shell Rg shell_rg46.41
Envelope Rg envelope_rg42.06
Shape Rg shape_rg43.77
Total Rg total_rg43.96
Total atoms total_atoms3971
Residues n_residues513
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 dmax135.0
Rg (real space) rg_real44.12
Rg uncertainty (real space) rg_real_error1.37
I(0) (real space) i0_real5.3960e+07
I(0) uncertainty (real space) i0_real_error9.7550e+05
Rg (reciprocal space) rg_reciprocal43.52
I(0) (reciprocal space) i0_reciprocal53920000.0000
Solution quality estimate total_estimate0.5761
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.5
Skewness Skewness skewness0.335
Kurtosis Kurtosis kurtosis-1.007
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1262000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.138; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.069; Smooth: 0.004

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4i0ca_
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
Domain ID domain_idd4i0cb_
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
Domain ID domain_idd4i0cc1
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_idd4i0cc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4i0cd1
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_idd4i0cd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id4i0cA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id4i0cB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10
Domain ID domain_id4i0cC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4i0cD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)