SAXSdb — 3sc2

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

SERINE CARBOXYPEPTIDASE II (CPDW-II)

Triticum aestivum

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 6 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–259 Chain B； UniProt 266–417	Not recorded	;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 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 3SC2	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
1WHS 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 Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–260（255 aa） Chain B 266–418（153 aa）	Not recorded	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 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 Different structure-quality metrics	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 Different structure-quality metrics	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

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 1–259； UniProt 1–259 Author chain B； PDBConstruct 1–152； UniProt 266–417

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3sc2
Deposition date deposition_date	1992-07-01
Structure title title	REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-ANGSTROMS RESOLUTION
Keywords keywords	HYDROLASE(CARBOXYPEPTIDASE); HYDROLASE(CARBOXYPEPTIDASE)
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.08 Å
Radius of gyration Rg (electron density) rg_electron	20.84 Å
Forward intensity I(0) i0	37542600.00
Molecular weight molecular_weight	47184.0 kDa
Excluded volume excluded_volume	58775 Å³
Envelope volume envelope_volume	67056 Å³
Hydration-shell volume shell_volume	26030 Å³
Envelope diameter envelope_diameter	73.3 Å
Shell Rg shell_rg	28.36 Å
Envelope Rg envelope_rg	20.99 Å
Shape Rg shape_rg	20.81 Å
Total Rg total_rg	21.82 Å
Total atoms total_atoms	3336
Residues n_residues	394
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	69.5 Å
Rg (real space) rg_real	21.90 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	3.7540e+07
I(0) uncertainty (real space) i0_real_error	4.4240e+05
Rg (reciprocal space) rg_reciprocal	21.94 Å
I(0) (reciprocal space) i0_reciprocal	37540000.0000
Solution quality estimate total_estimate	0.8908
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.117
Kurtosis Kurtosis kurtosis	-0.419
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8823000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SERINE CARBOXYPEPTIDASE II (CPDW-II)
Molecular weight formula_weight	28705.8 kDa
EC 编号 ec_number	3.4.16.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3533

VEPSGHAADRIARLPGQPAVDFDMYSGYITVDEGAGRSLFYLLQEAPEDAQPAPLVLWLNGGPGCSSVAYGASEELGAFRVKPAGAGLVLNEYRWNKVANVLFLDSPAGVGFSYTNTSSDIYTSGDNRTAHDSYAFLAKWFERFPHYKYRDFYIAGESYAGHYVPELSQLVHRSKNPVINLKGFMVGNGLIDDYHDYVGTFEFWWNHGIVSDDTYRRLKEACLHDSFIHPSPACDAATDVATAEQGNIDMYSLYTPVCN

来源 Source

来源生物 organism	Triticum aestivum
通用名 common_name	bread wheat
NCBI Class编号 ncbi_taxonomy_id	4565

Entity 2 Entity 2 polymer

Description description	SERINE CARBOXYPEPTIDASE II (CPDW-II)
Molecular weight formula_weight	17192.4 kDa
EC 编号 ec_number	3.4.16.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SYDPCTERYSTAYYNRRDVQMALHANVTGAMNYTWATCSDTINTHWHDAPRSMLPIYRELIAAGLRIWVFSGDTDAVVPLTATRYSIGALGLPTTTSWYPWYDDQEVGGWSQVYKGLTLVSVRGAGHEVPLHRPRQALVLFQYFLQGKPMPG

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	197

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3sc2.1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.5 — Serine carboxypeptidase-like

CATH v4.4 (3 domains)

Domain ID domain_id	3sc2A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3sc2B01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	940 —

Domain ID domain_id	3sc2B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11320 —

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8. Citations (4)

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Unit-cell length a length_a	98.400 Å
Unit-cell length b length_b	98.400 Å
Unit-cell length c length_c	209.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1690
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/sc/3sc2/3sc2.fit
pddf	/app/data/pr_computation/sc/3sc2/3sc2.pr.out
profile	/app/data/saxs_computation/sc/3sc2/3sc2.dat

REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-ANGSTROMS RESOLUTION

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

SERINE CARBOXYPEPTIDASE II (CPDW-II)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)