SAXSdb — 1dtd

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

CARBOXYPEPTIDASE A2

OrganismNot specified

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 116–417	Not recorded	METALLOCARBOXYPEPTIDASE INHIBITOR × 1 （P81511） ZN ZINC ION × 1 GLU GLUTAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；298 K；ammonium phosphate, sodium citrate, pH 7.5, VAPOR DIFFUSION, temperature 298.0K	Resolution 1.65 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.

Other PDB	Difference from Current Entry 1DTD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AYE HUMAN PROCARBOXYPEPTIDASE A2 Deposited 1997-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–417（401 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 1.80 Å R-free 0.222
1O6X NMR solution structure of the activation domain of human procarboxypeptidase A2 Deposited 2002-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–94（78 aa） Fragment：ACTIVATION DOMAIN, RESIDUES 17-94	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50MM PHOSPHATE	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBPA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–303； UniProt 116–417

METALLOCARBOXYPEPTIDASE INHIBITOR

OrganismNot specified

UniProt P81511

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 20–80	Not recorded	CARBOXYPEPTIDASE A2 × 1 （P48052） ZN ZINC ION × 1 GLU GLUTAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；298 K；ammonium phosphate, sodium citrate, pH 7.5, VAPOR DIFFUSION, temperature 298.0K	Resolution 1.65 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.

Other PDB	Difference from Current Entry 1DTD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DTV NMR STRUCTURE OF THE LEECH CARBOXYPEPTIDASE INHIBITOR (LCI) Deposited 2000-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–81（67 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM Tris；Pressure ambient NMR sample composition 1 mM in 20 mM phosphate buffer, pH 6.5 \| 90% H2O/10% D2O	Resolution not provided
1ZFI Solution structure of the leech carboxypeptidase inhibitor Deposited 2005-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–81（66 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.5；300 K；Ionic strength (raw mmCIF value) 20mM phosphate buffer；Pressure ambient NMR sample composition 1mM 15N-labeled leech carboxypeptidase inhibitor; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM 15N-labeled leech carboxypeptidase inhibitor; 100% D2O \| 100% D2O	Resolution not provided
1ZFL Solution structure of III-A, the major intermediate in the oxidative folding of leech carboxypeptidase inhibitor Deposited 2005-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–81（66 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.5；300 K；Ionic strength (raw mmCIF value) 20mM phosphate buffer；Pressure ambient NMR sample composition 1mM 15N-labeled III-A intermediate; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM 15N-labeled III-A intermediate; 100% D2O \| 100% D2O	Resolution not provided
2ABZ Crystal structure of C19A/C43A mutant of leech carboxypeptidase inhibitor in complex with bovine carboxypeptidase A Deposited 2005-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 16–81（66 aa） Chain D 16–81（66 aa） Chain E 16–81（66 aa） Chain F 16–81（66 aa）	Mutation：C19A/C43A Mutation：C19A/C43A Mutation：C19A/C43A Mutation：C19A/C43A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；1.5M Lithium Sulfate monohydrate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.16 Å R-free 0.234

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

View Construct and Data Evidence

UniProt name	MCPI_HIRME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–61； UniProt 20–80

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	1dtd
Deposition date deposition_date	2000-01-12
Structure title title	CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE LEECH CARBOXYPEPTIDASE INHIBITOR AND THE HUMAN CARBOXYPEPTIDASE A2 (LCI-CPA2)
Keywords keywords	Carboxypeptidase A2, Leech Carboxypeptidase Inhibitor, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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	21.13 Å
Radius of gyration Rg (electron density) rg_electron	20.03 Å
Forward intensity I(0) i0	28116500.00
Molecular weight molecular_weight	40551.0 kDa
Excluded volume excluded_volume	50513 Å³
Envelope volume envelope_volume	56432 Å³
Hydration-shell volume shell_volume	23283 Å³
Envelope diameter envelope_diameter	72.2 Å
Shell Rg shell_rg	27.23 Å
Envelope Rg envelope_rg	20.34 Å
Shape Rg shape_rg	20.01 Å
Total Rg total_rg	20.96 Å
Total atoms total_atoms	2854
Residues n_residues	364
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	71.8 Å
Rg (real space) rg_real	21.05 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.8120e+07
I(0) uncertainty (real space) i0_real_error	3.6910e+05
Rg (reciprocal space) rg_reciprocal	21.07 Å
I(0) (reciprocal space) i0_reciprocal	28120000.0000
Solution quality estimate total_estimate	0.8593
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.5 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.106
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12430000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.958

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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	CARBOXYPEPTIDASE A2
Molecular weight formula_weight	33660.9 kDa
EC 编号 ec_number	3.4.15.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3085

FNFGAYHTLEEISQEMDNLVAEHPGLVSKVNIGSSFENRPMNVLKFSTGGDKPAIWLDAGIHAREWVTQATALWTANKIVSDYGKDPSITSILDALDIFLLPVTNPDGYVFSQTKNRMWRKTRSKVSAGSLCVGVDPNRNWDAGFGGPGASSNPCSDSYHGPSANSEVEVKSIVDFIKSHGKVKAFIILHSYSQLLMFPYGYKCTKLDDFDELSEVAQKAAQSLSRLHGTKYKVGPICSVIYQASGGSIDWSYDYGIKYSFAFELRDTGRYGFLLPARQILPTAEETWLGLKAIMEHVRDHPY

Entity 2 Entity 2 polymer

Description description	METALLOCARBOXYPEPTIDASE INHIBITOR
Molecular weight formula_weight	6787.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DESFLCYQPDQVCCFICRGAAPLPSEGECNPHPTAPWCREGAVEWVPYSTGQCRTTCIPYV

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
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	231

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dtda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.1 — Pancreatic carboxypeptidases

Domain ID domain_id	d1dtdb_
Class class	g — Small proteins
Fold Fold fold	g.30 — Carboxypeptidase inhibitor
Superfamily Superfamily superfamily	g.30.1 — Carboxypeptidase inhibitor
Family Family family	g.30.1.1 — Carboxypeptidase inhibitor

CATH v4.4 (2 domains)

Domain ID domain_id	1dtdA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1dtdB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	10 — Carboxypeptidase inhibitor

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8. Citations (1)

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Unit-cell length a length_a	80.439 Å
Unit-cell length b length_b	80.439 Å
Unit-cell length c length_c	114.464 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.2340

fit	/app/data/saxs_computation/dt/1dtd/1dtd.fit
pddf	/app/data/pr_computation/dt/1dtd/1dtd.pr.out
profile	/app/data/saxs_computation/dt/1dtd/1dtd.dat

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE LEECH CARBOXYPEPTIDASE INHIBITOR AND THE HUMAN CARBOXYPEPTIDASE A2 (LCI-CPA2)

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

CARBOXYPEPTIDASE A2

State in the Current Structure

Other States of the Same Protein in the Database

METALLOCARBOXYPEPTIDASE INHIBITOR

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)