1op9

Complex of human lysozyme with camelid VHH HL6 antibody fragment

Method: X-RAY DIFFRACTION Dmax: 74.7 Å Quality: GOOD

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 B; UniProt 19–148 Not recorded HL6 camel VHH fragment × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;20 % W/V PEG4000, 0.2M imidazole malate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.86 Å R-free 0.238

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 219 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges 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 1op9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1op9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1op9
Deposition date deposition_date2003-03-05
Structure title titleComplex of human lysozyme with camelid VHH HL6 antibody fragment
Keywords keywordsantigen-antibody complex, immunoglobulin, amyloid fibril formation inhibition, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.99
Radius of gyration Rg (electron density) rg_electron20.15
Forward intensity I(0) i015136400.00
Molecular weight molecular_weight27719.0 kDa
Excluded volume excluded_volume33977 ų
Envelope volume envelope_volume39713 ų
Hydration-shell volume shell_volume17396 ų
Envelope diameter envelope_diameter73.7
Shell Rg shell_rg25.58
Envelope Rg envelope_rg20.50
Shape Rg shape_rg20.12
Total Rg total_rg20.97
Total atoms total_atoms1945
Residues n_residues251
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 dmax74.7
Rg (real space) rg_real21.08
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real1.5140e+07
I(0) uncertainty (real space) i0_real_error2.3900e+05
Rg (reciprocal space) rg_reciprocal21.06
I(0) (reciprocal space) i0_reciprocal15140000.0000
Solution quality estimate total_estimate0.8459
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.6
Skewness Skewness skewness0.460
Kurtosis Kurtosis kurtosis-0.279
Angular range angular_range— – 0.3800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3102000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.718; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1op9a1
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_idd1op9a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1op9b_
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 (2 domains)

Domain ID domain_id1op9A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1op9B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)