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1svz

Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-2 protease

Method: X-RAY DIFFRACTION Dmax: 75.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

single-chain Fv fragment 1696

Mus musculus

UniProt P01631

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 4–112 Chain B； UniProt 4–112 Fragment：scFv1696 epitope peptide corresponding to N-terminus of HIV-2 protease × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.6；292 K；protein concentration 14mg/ml, 0.05M tri-sodium citrate, 0.1M sodium phosphate, 27% PEG 3400, 0.2M ammonium sulfate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 1.89 Å R-free 0.239

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.

Other PDB Difference from Current Entry 1SVZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BFV MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI Deposited 1997-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–113（113 aa） Fragment：MONOCLONAL ANTIBODY FV FRAGMENT
Not recorded ZN ZINC ION × 3 STG ESTRIOL 3-(B-D-GLUCURONIDE) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5
Resolution 2.10 Å R-free 0.271
1BFV MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI Deposited 1997-05-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–113（113 aa） Fragment：MONOCLONAL ANTIBODY FV FRAGMENT
Not recorded ZN ZINC ION × 6 STG ESTRIOL 3-(B-D-GLUCURONIDE) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5
Resolution 2.10 Å R-free 0.271
1BFV MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI Deposited 1997-05-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–113（113 aa） Fragment：MONOCLONAL ANTIBODY FV FRAGMENT
Not recorded ZN ZINC ION × 6 STG ESTRIOL 3-(B-D-GLUCURONIDE) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5
Resolution 2.10 Å R-free 0.271
1BFV MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI Deposited 1997-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–113（113 aa） Fragment：MONOCLONAL ANTIBODY FV FRAGMENT
Not recorded ZN ZINC ION × 3 STG ESTRIOL 3-(B-D-GLUCURONIDE) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5
Resolution 2.10 Å R-free 0.271
1CFV MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI Deposited 1997-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–113（113 aa） Fragment：FV FRAGMENT
Not recorded ZN ZINC ION × 3 E3G ESTRONE BETA-D-GLUCURONIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.0
Resolution 2.10 Å R-free 0.247
1MAJ SOLUTION STRUCTURE OF AN ISOLATED ANTIBODY VL DOMAIN Deposited 1993-09-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–113（113 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1MAK SOLUTION STRUCTURE OF AN ISOLATED ANTIBODY VL DOMAIN Deposited 1993-09-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–113（113 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2BFV MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI Deposited 1997-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–113（113 aa） Fragment：MONOCLONAL ANTIBODY FV FRAGMENT
Not recorded STG ESTRIOL 3-(B-D-GLUCURONIDE) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 15% (W/V) PEG 4000, 100MM NA ACETATE AND 50MM TRIS HCL PH 8.5
Resolution 2.50 Å
2DLF HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 6.75 Deposited 1998-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–113（113 aa） Fragment：FV FRAGMENT (VL DOMAIN) SYNONYM: ANTI-DANSYL FV FRAGMENT
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.75；CRYSTALLIZATION CONDITIONS: TEMPERATURE AT 20C. PRECIPITANT SOLUTION CONTAINED 1 AMMONIUM SULFATE AND 0.025 M SODIUM CACODYLATE (PH 6.75). 5 MG/ML OF FV FRAGMENT., VAPOR DIFFUSION, HANGING DROP
Resolution 1.55 Å R-free 0.233

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KV2A7_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–112； UniProt 4–112 Author chain B； PDBConstruct 4–112； UniProt 4–112

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 1svz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1svz
Deposition date deposition_date2004-03-30
Structure title titleCrystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-2 protease
Keywords keywordsantibody-antigen complex; HIV inhibiting antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.37 Å
Radius of gyration Rg (electron density) rg_electron23.09 Å
Forward intensity I(0) i046874900.00
Molecular weight molecular_weight53324.0 kDa
Excluded volume excluded_volume66622 ų
Envelope volume envelope_volume77513 ų
Hydration-shell volume shell_volume27838 ų
Envelope diameter envelope_diameter76.5 Å
Shell Rg shell_rg30.27 Å
Envelope Rg envelope_rg22.85 Å
Shape Rg shape_rg23.09 Å
Total Rg total_rg23.90 Å
Total atoms total_atoms3770
Residues n_residues476
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax75.6 Å
Rg (real space) rg_real24.25 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real4.6870e+07
I(0) uncertainty (real space) i0_real_error6.5470e+05
Rg (reciprocal space) rg_reciprocal24.28 Å
I(0) (reciprocal space) i0_reciprocal46880000.0000
Solution quality estimate total_estimate0.9080
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.2 Å
Skewness Skewness skewness0.197
Kurtosis Kurtosis kurtosis-0.462
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11670000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1svza1
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_idd1svza2
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_idd1svzb1
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_idd1svzb2
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)

CATH v4.4 (4 domains)

Domain ID domain_id1svzA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1svzA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1svzB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1svzB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)