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5a2j

Crystal structure of scFv-SM3 in complex with the naked peptide APDTRP

Method: X-RAY DIFFRACTION Dmax: 57.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SCFV-SM3

MUS MUSCULUS

UniProt P01727

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 20–117 Fragment：RESIDUES 6-115,20-129 THE NAKED PEPTIDE APDTRP × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.65 Å R-free 0.197

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 5A2J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5A2I Crystal structure of scFv-SM3 in complex with APD-SGalNAc-RP Deposited 2015-05-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 20–129（110 aa） Fragment：RESIDUES 6-115,20-129
Not recorded EDO 1,2-ETHANEDIOL × 2 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.88 Å R-free 0.261
5A2K Crystal structure of scFv-SM3 in complex with APD-TGalNAc-RP Deposited 2015-05-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 20–129（110 aa） Fragment：RESIDUES 6-115,20-129
Not recorded EDO 1,2-ETHANEDIOL × 6 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.216
5A2L Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP Deposited 2015-05-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 20–129（110 aa） Fragment：RESIDUES 6-115,20-129
Not recorded EDO 1,2-ETHANEDIOL × 4 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.79 Å R-free 0.204
5N7B Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody Deposited 2017-02-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 19–129（111 aa）
Not recorded EDO 1,2-ETHANEDIOL × 7 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M disodium hydrogen phosphate
Resolution 1.70 Å R-free 0.211

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LV1E_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain H； PDBConstruct 136–231； UniProt 20–117

SCFV-SM3

MUS MUSCULUS

UniProt P01801

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 6–115 Fragment：RESIDUES 6-115,20-129 THE NAKED PEPTIDE APDTRP × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.65 Å R-free 0.197

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 5A2J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1SM3 CRYSTAL STRUCTURE OF THE TUMOR SPECIFIC ANTIBODY SM3 COMPLEX WITH ITS PEPTIDE EPITOPE Deposited 1997-12-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 2–220（219 aa） Fragment：FAB FRAGMENT
Not recorded CD CADMIUM ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 1.95 Å R-free 0.283
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–115（115 aa） Fragment：FV FRAGMENT (VH 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
5A2I Crystal structure of scFv-SM3 in complex with APD-SGalNAc-RP Deposited 2015-05-20 Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 6–115（110 aa） Fragment：RESIDUES 6-115,20-129
Not recorded EDO 1,2-ETHANEDIOL × 2 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.88 Å R-free 0.261
5A2K Crystal structure of scFv-SM3 in complex with APD-TGalNAc-RP Deposited 2015-05-20 Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 6–115（110 aa） Fragment：RESIDUES 6-115,20-129
Not recorded EDO 1,2-ETHANEDIOL × 6 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.216
5A2L Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP Deposited 2015-05-20 Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 6–115（110 aa） Fragment：RESIDUES 6-115,20-129
Not recorded EDO 1,2-ETHANEDIOL × 4 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.79 Å R-free 0.204
5N7B Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody Deposited 2017-02-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–114（114 aa）
Not recorded EDO 1,2-ETHANEDIOL × 7 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M disodium hydrogen phosphate
Resolution 1.70 Å R-free 0.211
5OWP Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3 Deposited 2017-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 6–111（106 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 3350, disodium hydrogen phosphate
Resolution 1.85 Å R-free 0.256

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

View Construct and Data Evidence
UniProt name HVM32_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain H； PDBConstruct 6–117； UniProt 6–115

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 5a2j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5a2j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5a2j
Deposition date deposition_date2015-05-20
Structure title titleCrystal structure of scFv-SM3 in complex with the naked peptide APDTRP
Keywords keywordsPEPTIDE BINDING PROTEIN, GLYCOPEPTIDES, ANTIBODIES, MOLECULAR RECOGNITION, CONFORMATION ANALYSIS, FUSION PROTEIN; PEPTIDE BINDING PROTEIN
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_guinier18.23 Å
Radius of gyration Rg (electron density) rg_electron17.19 Å
Forward intensity I(0) i011775000.00
Molecular weight molecular_weight25168.0 kDa
Excluded volume excluded_volume31279 ų
Envelope volume envelope_volume34998 ų
Hydration-shell volume shell_volume17105 ų
Envelope diameter envelope_diameter59.1 Å
Shell Rg shell_rg23.20 Å
Envelope Rg envelope_rg17.47 Å
Shape Rg shape_rg17.13 Å
Total Rg total_rg18.27 Å
Total atoms total_atoms1773
Residues n_residues221
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 dmax57.4 Å
Rg (real space) rg_real18.15 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real1.1770e+07
I(0) uncertainty (real space) i0_real_error1.4170e+05
Rg (reciprocal space) rg_reciprocal18.16 Å
I(0) (reciprocal space) i0_reciprocal11780000.0000
Solution quality estimate total_estimate0.8968
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.217
Kurtosis Kurtosis kurtosis-0.384
Angular range angular_range— – 0.4350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3843000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.946
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5a2jH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5a2jH02
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)