SAXSdb — 4bd9

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

CARBOXYPEPTIDASE A4

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CARBOXYPEPTIDASE INHIBITOR SMCI × 1 （P84875） ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBPA4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–310； UniProt 112–421

CARBOXYPEPTIDASE INHIBITOR SMCI

SABELLASTARTE MAGNIFICA

UniProt P84875

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CARBOXYPEPTIDASE A4 × 1 （Q9UI42） ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCPI_SABMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–165； UniProt 1–165

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	4bd9
Deposition date deposition_date	2012-10-05
Structure title title	Structure of the complex between SmCI and human carboxypeptidase A4
Keywords keywords	HYDROLASE-HYDROLASE INHIBITOR COMPLEX, SERINE PROTEASE INHIBITOR; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4bd9__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4bd9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bd9__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	23.55 Å
Rg (electron density)	22.68 Å
Total Rg	23.60 Å
Atom count	3706
Residues	469
Excluded volume	65034 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bd9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CARBOXYPEPTIDASE A4
Molecular weight formula_weight	34851.0 kDa
EC 编号 ec_number	3.4.17.-
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	3829

ERSSNNFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNLY

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	KOMAGATAELLA PASTORIS

Entity 2 Entity 2 polymer

Description description	CARBOXYPEPTIDASE INHIBITOR SMCI
Molecular weight formula_weight	18624.6 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ISVCDLPADRGQCTAYIPQWFFAKTTEDCEKFVYGGCQGNANRFETKDDCIANCGCNLPSKVGPCRVSARMWFHNPETEKCEVFIYGGCHGNANRFATETECQEVCDRYQKPGFCYQPSETGPCKGSFPRYYYDYEDGECKEFIYGGCEGNANNFETKESCENAC

Source Source

Source organism organism	SABELLASTARTE MAGNIFICA
NCBI taxonomy ID ncbi_taxonomy_id	389514
Host organism host_organism	KOMAGATAELLA PASTORIS

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	123

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4bd9b1
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

Domain ID domain_id	d4bd9b2
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

Domain ID domain_id	d4bd9b3
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	4bd9A00
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	4bd9B01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	4bd9B02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	4bd9B03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

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Unit-cell length a length_a	138.670 Å
Unit-cell length b length_b	138.670 Å
Unit-cell length c length_c	161.560 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	38.856 Å
R factor r_factor	0.2247
R_work r_work	0.2231
R_free r_free	0.2538

Structure of the complex between SmCI and human carboxypeptidase A4

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

CARBOXYPEPTIDASE A4

State in the Current Structure

Other States of the Same Protein in the Database

CARBOXYPEPTIDASE INHIBITOR SMCI

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4bd9__assembly_1__model_1

4bd9__assembly_1__model_1 | I(q)

4bd9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the complex between SmCI and human carboxypeptidase A4

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

CARBOXYPEPTIDASE A4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CARBOXYPEPTIDASE INHIBITOR SMCI

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4bd9__assembly_1__model_1

4bd9__assembly_1__model_1 | I(q)

4bd9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)