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1whs

STRUCTURE OF THE COMPLEX OF L-BENZYLSUCCINATE WITH WHEAT SERINE CARBOXYPEPTIDASE II AT 2.0 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 65.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SERINE CARBOXYPEPTIDASE II

Triticum aestivum

UniProt P08819

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 4 其他Polymer 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 6–260 Chain B； UniProt 266–418 Not recorded alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2 ACY ACETIC ACID × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å

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 1WHS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BCR COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, ANTIPAIN, AND ARGININE AT ROOM TEMPERATURE Deposited 1995-11-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–263（263 aa）
Chain B 264–423（160 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ARG ARGININE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1BCS COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, CHYMOSTATIN, AND ARGININE AT 100 DEGREES KELVIN Deposited 1995-11-03 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–263（263 aa）
Chain B 264–423（160 aa）
Not recorded ARG ARGININE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2 ACT ACETATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.08 Å
1WHT STRUCTURE OF THE COMPLEX OF L-BENZYLSUCCINATE WITH WHEAT SERINE CARBOXYPEPTIDASE II AT 2.0 ANGSTROMS RESOLUTION Deposited 1994-03-07 Different construct Different ligand/ion Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 5–260（256 aa）
Chain B 266–418（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BZS L-BENZYLSUCCINIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1WHT STRUCTURE OF THE COMPLEX OF L-BENZYLSUCCINATE WITH WHEAT SERINE CARBOXYPEPTIDASE II AT 2.0 ANGSTROMS RESOLUTION Deposited 1994-03-07 Different construct Different oligomeric state Different ligand/ion Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–260（256 aa）
Chain B 266–418（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BZS L-BENZYLSUCCINIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
3SC2 REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-ANGSTROMS RESOLUTION Deposited 1992-07-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–259（259 aa）
Chain B 266–417（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CBP2_WHEAT
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–255； UniProt 6–260 Author chain B； PDBConstruct 1–153； UniProt 266–418

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 1whs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1whs
Deposition date deposition_date1994-03-07
Structure title titleSTRUCTURE OF THE COMPLEX OF L-BENZYLSUCCINATE WITH WHEAT SERINE CARBOXYPEPTIDASE II AT 2.0 ANGSTROMS RESOLUTION
Keywords keywordsSERINE CARBOXYPEPTIDASE; SERINE CARBOXYPEPTIDASE
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_guinier21.68 Å
Radius of gyration Rg (electron density) rg_electron20.48 Å
Forward intensity I(0) i036510400.00
Molecular weight molecular_weight46651.0 kDa
Excluded volume excluded_volume58132 ų
Envelope volume envelope_volume64325 ų
Hydration-shell volume shell_volume25405 ų
Envelope diameter envelope_diameter66.9 Å
Shell Rg shell_rg27.90 Å
Envelope Rg envelope_rg20.61 Å
Shape Rg shape_rg20.46 Å
Total Rg total_rg21.42 Å
Total atoms total_atoms3300
Residues n_residues396
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 dmax65.6 Å
Rg (real space) rg_real21.50 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real3.6510e+07
I(0) uncertainty (real space) i0_real_error4.1710e+05
Rg (reciprocal space) rg_reciprocal21.53 Å
I(0) (reciprocal space) i0_reciprocal36510000.0000
Solution quality estimate total_estimate0.9013
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.099
Kurtosis Kurtosis kurtosis-0.449
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7629000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.968
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1whs.1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.5 — Serine carboxypeptidase-like

CATH v4.4 (3 domains)

Domain ID domain_id1whsA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id1whsB01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily940 —
Domain ID domain_id1whsB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11320 —
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8. Citations (4)

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9. Files and Curves (10)