4kvc

2H2 Fab fragment of immature Dengue virus

Method: X-RAY DIFFRACTION Dmax: 77.9 Å Quality: EXCELLENT

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

Ig heavy chain V region MOPC 21, Igh protein

Mus musculus

UniProt P01783

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 17–119 Not recorded Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain × 1 (P01634,Q7TS98) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;25% PEG 6000 0.1 M MES 0.2M NH4Cl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.234

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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HVM16_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain H; PDBConstruct 1–103; UniProt 17–119

Ig heavy chain V region MOPC 21, Igh protein

Mus musculus

UniProt Q6PIP8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 120–230 Not recorded Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain × 1 (P01634,Q7TS98) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;25% PEG 6000 0.1 M MES 0.2M NH4Cl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.234

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.

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

View Construct and Data Evidence
UniProt name Q6PIP8_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain H; PDBConstruct 106–216; UniProt 120–230

Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain

Mus musculus

UniProt P01634

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 30–136 Not recorded Ig heavy chain V region MOPC 21, Igh protein × 1 (P01783,Q6PIP8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;25% PEG 6000 0.1 M MES 0.2M NH4Cl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.234

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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KV5A2_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain L; PDBConstruct 1–107; UniProt 30–136

Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain

Mus musculus

UniProt Q7TS98

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 130–234 Not recorded Ig heavy chain V region MOPC 21, Igh protein × 1 (P01783,Q6PIP8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;25% PEG 6000 0.1 M MES 0.2M NH4Cl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.31 Å R-free 0.234

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 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q7TS98_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain L; PDBConstruct 108–212; UniProt 130–234

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 4kvc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4kvc
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4kvc
Deposition date deposition_date2013-05-22
Structure title title2H2 Fab fragment of immature Dengue virus
Keywords keywordsFab fragment, immature Dengue, pr peptide, 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_guinier25.13
Radius of gyration Rg (electron density) rg_electron24.17
Forward intensity I(0) i038716900.00
Molecular weight molecular_weight46994.0 kDa
Excluded volume excluded_volume58269 ų
Envelope volume envelope_volume71890 ų
Hydration-shell volume shell_volume24956 ų
Envelope diameter envelope_diameter80.5
Shell Rg shell_rg31.30
Envelope Rg envelope_rg23.96
Shape Rg shape_rg24.16
Total Rg total_rg25.00
Total atoms total_atoms6491
Residues n_residues432
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 dmax77.9
Rg (real space) rg_real25.10
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real3.8720e+07
I(0) uncertainty (real space) i0_real_error4.9850e+05
Rg (reciprocal space) rg_reciprocal25.11
I(0) (reciprocal space) i0_reciprocal38720000.0000
Solution quality estimate total_estimate0.9120
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4
Skewness Skewness skewness0.259
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8312000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.971

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4kvch_
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_idd4kvcl1
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_idd4kvcl2
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 (4 domains)

Domain ID domain_id4kvcH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4kvcH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4kvcL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4kvcL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)