2eks

Crystal structure of humanized HyHEL-10 FV-HEN lysozyme complex

Method: X-RAY DIFFRACTION Dmax: 69.4 Å Quality: EXCELLENT

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

Lysozyme C

OrganismNot specified

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 ANTI-LYSOZYME ANTIBODY FV REGION × 1 ANTI-LYSOZYME ANTIBODY FV REGION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;28-31% PEGMME 550, 0.01M zinc sulfate, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K Resolution 2.00 Å R-free 0.265

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 2eks

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2eks
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2eks
Deposition date deposition_date2007-03-24
Structure title titleCrystal structure of humanized HyHEL-10 FV-HEN lysozyme complex
Keywords keywordsIMMUNE SYSTEM, HYDROLASE, 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_guinier21.83
Radius of gyration Rg (electron density) rg_electron20.89
Forward intensity I(0) i027202700.00
Molecular weight molecular_weight38444.0 kDa
Excluded volume excluded_volume47476 ų
Envelope volume envelope_volume54499 ų
Hydration-shell volume shell_volume21976 ų
Envelope diameter envelope_diameter71.2
Shell Rg shell_rg27.27
Envelope Rg envelope_rg21.14
Shape Rg shape_rg20.82
Total Rg total_rg21.89
Total atoms total_atoms2702
Residues n_residues349
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 dmax69.4
Rg (real space) rg_real21.74
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real2.7200e+07
I(0) uncertainty (real space) i0_real_error3.4010e+05
Rg (reciprocal space) rg_reciprocal21.76
I(0) (reciprocal space) i0_reciprocal27200000.0000
Solution quality estimate total_estimate0.9043
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9
Skewness Skewness skewness0.212
Kurtosis Kurtosis kurtosis-0.470
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5101000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2eksa_
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_idd2eksb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd2eksb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2eksc_
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 (3 domains)

Domain ID domain_id2eksA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2eksB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2eksC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)