SAXSdb — 1pok

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

Isoaspartyl dipeptidase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 ZINC ION × 2 ASPARAGINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 ZINC ION × 2 ASPARAGINE × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	SULFATE ION × 8 ZINC ION × 16 ASPARAGINE × 8 water × 8	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 ZINC ION × 4 ASPARAGINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IADA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–390； UniProt 1–390 Author chain B； PDBConstruct 1–390； UniProt 1–390

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	1pok
Deposition date deposition_date	2003-06-15
Structure title title	Crystal structure of Isoaspartyl Dipeptidase
Keywords keywords	HYDROLASE; HYDROLASE
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.

1pok__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1pok__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pok__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	43.27 Å
Rg (electron density)	43.01 Å
Total Rg	43.28 Å
Atom count	22264
Residues	2996
Excluded volume	397400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pok__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1pok__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1pok__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1pok__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	Isoaspartyl dipeptidase
Molecular weight formula_weight	41167.8 kDa
EC 编号 ec_number	3.4.19.-
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	5655

MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFETA

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	4

Entity 4 Entity 4 non-polymer

Description description	ASPARAGINE
Molecular weight formula_weight	132.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1poka1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.7 — Isoaspartyl dipeptidase

Domain ID domain_id	d1poka2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.13 — Isoaspartyl dipeptidase, catalytic domain

Domain ID domain_id	d1pokb1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.7 — Isoaspartyl dipeptidase

Domain ID domain_id	d1pokb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.13 — Isoaspartyl dipeptidase, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1pokA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1pokA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	1pokB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1pokB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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Unit-cell length a length_a	117.475 Å
Unit-cell length b length_b	117.475 Å
Unit-cell length c length_c	137.955 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	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2090
R_free r_free	0.2660

Crystal structure of Isoaspartyl Dipeptidase

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

Isoaspartyl dipeptidase

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

1pok__assembly_3__model_1

1pok__assembly_3__model_1 | I(q)

1pok__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Isoaspartyl Dipeptidase

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

Isoaspartyl dipeptidase

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

1pok__assembly_3__model_1

1pok__assembly_3__model_1 | I(q)

1pok__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)