1a2y

HEN EGG WHITE LYSOZYME, D18A MUTANT, IN COMPLEX WITH MOUSE MONOCLONAL ANTIBODY D1.3

Method: X-RAY DIFFRACTION Dmax: 80.9 Å Quality: GOOD

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

IGG1-KAPPA D1.3 FV (LIGHT CHAIN)

Mus musculus

UniProt P01635

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 1–108 Not recorded IGG1-KAPPA D1.3 FV (HEAVY CHAIN) × 1 (P01820) LYSOZYME × 1 (P00698) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 1.50 Å R-free 0.251

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.

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KV5C_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–107; UniProt 1–108

IGG1-KAPPA D1.3 FV (HEAVY CHAIN)

Mus musculus

UniProt P01820

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 20–115 Not recorded IGG1-KAPPA D1.3 FV (LIGHT CHAIN) × 1 (P01635) LYSOZYME × 1 (P00698) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 1.50 Å R-free 0.251

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.

14 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HV44_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–96; UniProt 20–115

LYSOZYME

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:D18A IGG1-KAPPA D1.3 FV (LIGHT CHAIN) × 1 (P01635) IGG1-KAPPA D1.3 FV (HEAVY CHAIN) × 1 (P01820) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;pH 6.5 Resolution 1.50 Å R-free 0.251

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 1a2y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a2y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1a2y
Deposition date deposition_date1998-01-13
Structure title titleHEN EGG WHITE LYSOZYME, D18A MUTANT, IN COMPLEX WITH MOUSE MONOCLONAL ANTIBODY D1.3
Keywords keywords;COMPLEX (IMMUNOGLOBULIN-HYDROLASE), IMMUNOGLOBULIN V REGION, HYDROLASE, GLYCOSIDASE, BACTERIOLYTIC ENZYME, EGG WHITE, COMPLEX (IMMUNOGLOBULIN-HYDROLASE) complex ;; COMPLEX (IMMUNOGLOBULIN/HYDROLASE)
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.59
Radius of gyration Rg (electron density) rg_electron22.76
Forward intensity I(0) i028348400.00
Molecular weight molecular_weight38913.0 kDa
Excluded volume excluded_volume47938 ų
Envelope volume envelope_volume58430 ų
Hydration-shell volume shell_volume22409 ų
Envelope diameter envelope_diameter83.3
Shell Rg shell_rg28.75
Envelope Rg envelope_rg22.92
Shape Rg shape_rg22.71
Total Rg total_rg23.65
Total atoms total_atoms2733
Residues n_residues352
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 dmax80.9
Rg (real space) rg_real23.64
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real2.8350e+07
I(0) uncertainty (real space) i0_real_error3.1800e+05
Rg (reciprocal space) rg_reciprocal23.63
I(0) (reciprocal space) i0_reciprocal28350000.0000
Solution quality estimate total_estimate0.8732
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.3
Skewness Skewness skewness0.405
Kurtosis Kurtosis kurtosis-0.320
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7138000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.988

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1a2ya_
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_idd1a2yb_
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_idd1a2yc_
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_id1a2yA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1a2yB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1a2yC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (4)

9. Files and Curves (10)