SAXSdb — 7pc9

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

Synaptojanin-2-binding protein,Annexin A2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	CALCIUM ION × 5 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Protein Tax-1 × 1 （P03409） CALCIUM ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ANXA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 105–415； UniProt 29–339 Author chain B； PDBConstruct 105–415； UniProt 29–339

Synaptojanin-2-binding protein,Annexin A2

Homo sapiens

UniProt P57105

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	CALCIUM ION × 5 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Protein Tax-1 × 1 （P03409） CALCIUM ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYJ2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–102； UniProt 6–103 Author chain B； PDBConstruct 5–102； UniProt 6–103

Protein Tax-1

OrganismNot specified

UniProt P03409

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
2	Insufficient information	Heteromer	Protein 2	Synaptojanin-2-binding protein,Annexin A2 × 1 （P07355,P57105） CALCIUM ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TAX_HTL1A
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 344–353

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	7pc9
Deposition date deposition_date	2021-08-03
Structure title title	The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1
Keywords keywords	PDZ, complex, crystallization chaperone, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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.

7pc9__assembly_1__model_1

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

Download this curve (.dat)

7pc9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7pc9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.93 Å
Rg (electron density)	27.64 Å
Total Rg	28.08 Å
Atom count	3165
Residues	397
Excluded volume	56364 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7pc9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7pc9__assembly_2__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	Synaptojanin-2-binding protein,Annexin A2
Molecular weight formula_weight	47040.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	6854

GSHMDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQGSAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD

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

Entity 2 Entity 2 polymer

Description description	Protein Tax-1
Molecular weight formula_weight	1264.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SEKHFRETEV

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	363

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	7pc9A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	7pc9A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	7pc9A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	7pc9A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	7pc9B01
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	7pc9B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	7pc9B03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	7pc9B04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	7pc9B05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

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Unit-cell length a length_a	59.990 Å
Unit-cell length b length_b	99.850 Å
Unit-cell length c length_c	173.340 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	49.327 Å
R factor r_factor	0.2045
R_work r_work	0.2025
R_free r_free	0.2430

The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1

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

Synaptojanin-2-binding protein,Annexin A2

State in the Current Structure

Other States of the Same Protein in the Database

Synaptojanin-2-binding protein,Annexin A2

State in the Current Structure

Other States of the Same Protein in the Database

Protein Tax-1

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

7pc9__assembly_1__model_1

7pc9__assembly_1__model_1 | I(q)

7pc9__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1

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

Synaptojanin-2-binding protein,Annexin A2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Synaptojanin-2-binding protein,Annexin A2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein Tax-1

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

7pc9__assembly_1__model_1

7pc9__assembly_1__model_1 | I(q)

7pc9__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)