SAXSdb — 2v90

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

PDZ DOMAIN-CONTAINING PROTEIN 3

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDZD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–92； UniProt 246–335 Author chain B； PDBConstruct 3–92； UniProt 246–335 Author chain C； PDBConstruct 3–92； UniProt 246–335 Author chain D； PDBConstruct 3–92； UniProt 246–335 Author chain E； PDBConstruct 3–92； UniProt 246–335 Author chain F； PDBConstruct 3–92； UniProt 246–335

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	2v90
Deposition date deposition_date	2007-08-16
Structure title title	Crystal structure of the 3rd PDZ domain of intestine- and kidney- enriched PDZ domain IKEPP (PDZD3)
Keywords keywords	PDZD3, MEMBRANE, PDZ DOMAIN, PROTEIN-BINDING, PROTEIN BINDING; PROTEIN BINDING
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.

2v90__assembly_1__model_1

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

Download this curve (.dat)

2v90__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v90__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.63 Å
Rg (electron density)	20.53 Å
Total Rg	21.46 Å
Atom count	2111
Residues	283
Excluded volume	37142 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v90__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2v90__assembly_2__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	PDZ DOMAIN-CONTAINING PROTEIN 3
Molecular weight formula_weight	10257.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4638

SMKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADRETSV

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

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	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	388

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2v90a_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2v90b_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2v90c_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2v90d_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2v90e_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2v90f_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2v90A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2v90B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2v90C00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2v90D00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2v90E00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2v90F00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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Unit-cell length a length_a	48.150 Å
Unit-cell length b length_b	97.950 Å
Unit-cell length c length_c	59.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1960
R_work r_work	0.1930
R_free r_free	0.2560

Crystal structure of the 3rd PDZ domain of intestine- and kidney- enriched PDZ domain IKEPP (PDZD3)

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

PDZ DOMAIN-CONTAINING PROTEIN 3

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

2v90__assembly_1__model_1

2v90__assembly_1__model_1 | I(q)

2v90__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the 3rd PDZ domain of intestine- and kidney- enriched PDZ domain IKEPP (PDZD3)

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

PDZ DOMAIN-CONTAINING PROTEIN 3

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

2v90__assembly_1__model_1

2v90__assembly_1__model_1 | I(q)

2v90__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)