1hq4

STRUCTURE OF NATIVE CATALYTIC ANTIBODY HA5-19A4

Method: X-RAY DIFFRACTION Dmax: 97.7 Å Quality: GOOD

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

ANTIBODY HA5-19A4 FAB LIGHT CHAIN

OrganismNot specified

UniProt Q91W12

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 24–235 Fragment:VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS ANTIBODY HA5-19A4 FAB HEAVY CHAIN × 1 (P01867) CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.2;298 K;PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å R-free 0.265
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 24–235 Fragment:VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS ANTIBODY HA5-19A4 FAB HEAVY CHAIN × 1 (P01867) CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.2;298 K;PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q91W12_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–215; UniProt 24–235 Author chain C; PDBConstruct 2–215; UniProt 24–235

ANTIBODY HA5-19A4 FAB HEAVY CHAIN

OrganismNot specified

UniProt P01867

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 1–99 Fragment:VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS ANTIBODY HA5-19A4 FAB LIGHT CHAIN × 1 (Q91W12) CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.2;298 K;PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å R-free 0.265
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–99 Fragment:VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS ANTIBODY HA5-19A4 FAB LIGHT CHAIN × 1 (Q91W12) CD CADMIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.2;298 K;PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 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.

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GCBM_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 117–215; UniProt 1–99 Author chain D; PDBConstruct 117–215; UniProt 1–99

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 1hq4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1hq4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1hq4
Deposition date deposition_date2000-12-14
Structure title titleSTRUCTURE OF NATIVE CATALYTIC ANTIBODY HA5-19A4
Keywords keywordsCATALYTIC ANTIBODY, TERPENOID SYNTHASE, CARBOCATION, CYCLIZATION CASCADE, IMMUNOGLOBULIN, 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_guinier31.49
Radius of gyration Rg (electron density) rg_electron30.50
Forward intensity I(0) i0144920000.00
Molecular weight molecular_weight93539.0 kDa
Excluded volume excluded_volume116080 ų
Envelope volume envelope_volume150230 ų
Hydration-shell volume shell_volume41289 ų
Envelope diameter envelope_diameter104.1
Shell Rg shell_rg37.58
Envelope Rg envelope_rg29.68
Shape Rg shape_rg30.48
Total Rg total_rg31.20
Total atoms total_atoms6568
Residues n_residues862
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 dmax97.7
Rg (real space) rg_real31.35
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real1.4490e+08
I(0) uncertainty (real space) i0_real_error2.1570e+06
Rg (reciprocal space) rg_reciprocal31.41
I(0) (reciprocal space) i0_reciprocal144900000.0000
Solution quality estimate total_estimate0.8960
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.0
Skewness Skewness skewness0.209
Kurtosis Kurtosis kurtosis-0.346
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16160000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.868

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1hq4a1
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_idd1hq4a2
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_idd1hq4b1
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_idd1hq4b2
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_idd1hq4c1
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_idd1hq4c2
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_idd1hq4d1
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_idd1hq4d2
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 (8 domains)

Domain ID domain_id1hq4A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1hq4A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1hq4B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1hq4B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1hq4C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1hq4C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1hq4D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1hq4D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)