1za6

The structure of an antitumor CH2-domain-deleted humanized antibody

Method: X-RAY DIFFRACTION Dmax: 161.2 Å Quality: GOOD

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

IGG Light chain

Homo sapiens

UniProt Q6GMV9

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 53–235 Chain C; UniProt 53–235 Not recorded IGG Heavy chain × 2 (Q6GMX6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;290 K;4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 Resolution 2.80 Å R-free 0.296
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 53–235 Chain G; UniProt 53–235 Not recorded IGG Heavy chain × 2 (Q6GMX6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;290 K;4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 Resolution 2.80 Å R-free 0.296
3 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric(16) Consistent with protein copy count Chain A; UniProt 53–235 Chain C; UniProt 53–235 Chain E; UniProt 53–235 Chain G; UniProt 53–235 Not recorded IGG Heavy chain × 8 (Q6GMX6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;290 K;4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 Resolution 2.80 Å R-free 0.296
4 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 53–235 Chain C; UniProt 53–235 Chain E; UniProt 53–235 Chain G; UniProt 53–235 Not recorded IGG Heavy chain × 4 (Q6GMX6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;290 K;4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 Resolution 2.80 Å R-free 0.296

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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6GMV9_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 38–220; UniProt 53–235 Author chain C; PDBConstruct 38–220; UniProt 53–235 Author chain E; PDBConstruct 38–220; UniProt 53–235 Author chain G; PDBConstruct 38–220; UniProt 53–235

IGG Heavy chain

Homo sapiens

UniProt Q6GMX6

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 225–465 Chain D; UniProt 225–465 Not recorded IGG Light chain × 2 (Q6GMV9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;290 K;4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 Resolution 2.80 Å R-free 0.296
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 225–465 Chain H; UniProt 225–465 Not recorded IGG Light chain × 2 (Q6GMV9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;290 K;4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 Resolution 2.80 Å R-free 0.296
3 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric(16) Consistent with protein copy count Chain B; UniProt 225–465 Chain D; UniProt 225–465 Chain F; UniProt 225–465 Chain H; UniProt 225–465 Not recorded IGG Light chain × 8 (Q6GMV9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;290 K;4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 Resolution 2.80 Å R-free 0.296
4 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 225–465 Chain D; UniProt 225–465 Chain F; UniProt 225–465 Chain H; UniProt 225–465 Not recorded IGG Light chain × 4 (Q6GMV9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.2;290 K;4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 Resolution 2.80 Å R-free 0.296

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.

18 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6GMX6_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 104–344; UniProt 225–465 Author chain D; PDBConstruct 104–344; UniProt 225–465 Author chain F; PDBConstruct 104–344; UniProt 225–465 Author chain H; PDBConstruct 104–344; UniProt 225–465

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 1za6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1za6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1za6
Deposition date deposition_date2005-04-05
Structure title titleThe structure of an antitumor CH2-domain-deleted humanized antibody
Keywords keywordsImmunoglobulin fold, CH2-domain-deletion, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier57.13
Radius of gyration Rg (electron density) rg_electron56.85
Forward intensity I(0) i0816072000.00
Molecular weight molecular_weight237610.0 kDa
Excluded volume excluded_volume296140 ų
Envelope volume envelope_volume466020 ų
Hydration-shell volume shell_volume66954 ų
Envelope diameter envelope_diameter172.3
Shell Rg shell_rg62.41
Envelope Rg envelope_rg54.20
Shape Rg shape_rg56.81
Total Rg total_rg57.11
Total atoms total_atoms16740
Residues n_residues2176
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 dmax161.2
Rg (real space) rg_real57.07
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real8.1610e+08
I(0) uncertainty (real space) i0_real_error1.6940e+07
Rg (reciprocal space) rg_reciprocal57.13
I(0) (reciprocal space) i0_reciprocal816100000.0000
Solution quality estimate total_estimate0.8437
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary80.6
Skewness Skewness skewness0.093
Kurtosis Kurtosis kurtosis-0.794
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35890000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.998; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

Domain ID domain_idd1za6a1
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_idd1za6a2
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_idd1za6b1
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_idd1za6b2
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_idd1za6b3
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_idd1za6c1
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_idd1za6c2
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_idd1za6d1
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_idd1za6d2
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_idd1za6d3
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_idd1za6e1
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_idd1za6e2
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_idd1za6f1
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_idd1za6f2
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_idd1za6f3
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_idd1za6g1
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_idd1za6g2
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_idd1za6h1
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_idd1za6h2
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_idd1za6h3
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)

CATH v4.4 (20 domains)

Domain ID domain_id1za6A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6B03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6D03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6F01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6F02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6F03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6G01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6G02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1za6H03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (2)

9. Files and Curves (10)