SAXSdb — 6hks

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

Tyrosine-protein phosphatase non-receptor type 3

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	Protein E6 × 1 （P03126） IODIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein E6 × 1 （P03126） IODIDE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Protein E6 × 1 （P03126） IODIDE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Protein E6 × 1 （P03126） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Protein E6 × 1 （P03126） IODIDE ION × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Protein E6 × 1 （P03126） IODIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PTN3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–114； UniProt 489–597 Author chain B； PDBConstruct 6–114； UniProt 489–597 Author chain C； PDBConstruct 6–114； UniProt 489–597 Author chain D； PDBConstruct 6–114； UniProt 489–597 Author chain E； PDBConstruct 6–114； UniProt 489–597 Author chain F； PDBConstruct 6–114； UniProt 489–597

Protein E6

Human papillomavirus type 16

UniProt P03126

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein phosphatase non-receptor type 3 × 1 （P26045） IODIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein phosphatase non-receptor type 3 × 1 （P26045） IODIDE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein phosphatase non-receptor type 3 × 1 （P26045） IODIDE ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein phosphatase non-receptor type 3 × 1 （P26045） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein phosphatase non-receptor type 3 × 1 （P26045） IODIDE ION × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein phosphatase non-receptor type 3 × 1 （P26045） IODIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VE6_HPV16
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–11； UniProt 148–158 Author chain H； PDBConstruct 1–11； UniProt 148–158 Author chain I； PDBConstruct 1–11； UniProt 148–158 Author chain J； PDBConstruct 1–11； UniProt 148–158 Author chain K； PDBConstruct 1–11； UniProt 148–158 Author chain L； PDBConstruct 1–11； UniProt 148–158

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	6hks
Deposition date deposition_date	2018-09-07
Structure title title	Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal peptide
Keywords keywords	PDZ domain Protein tyrosine phosphatase Human papillomavirus E6 oncoprotein PDZ binding motif, 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.

6hks__assembly_1__model_1

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

Download this curve (.dat)

6hks__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hks__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.46 Å
Rg (electron density)	12.86 Å
Total Rg	14.20 Å
Atom count	801
Residues	100
Excluded volume	14212 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hks__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6hks__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6hks__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6hks__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6hks__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6hks__assembly_6__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	Tyrosine-protein phosphatase non-receptor type 3
Molecular weight formula_weight	12709.2 kDa
EC 编号 ec_number	3.1.3.48
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	4993

GAMGSSTEDASQYYCDKNDNGDSYLVLIRITPDEDGKFGFNLKGGVDQKMPLVVSRINPESPADTCIPKLNEGDQIVLINGRDISEHTHDQVVMFIKASRESHSRELALVIRRR

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 polymer

Description description	Protein E6
Molecular weight formula_weight	1393.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

RSSRTRRETQL

Source Source

Source organism organism	Human papillomavirus type 16
NCBI taxonomy ID ncbi_taxonomy_id	333760
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	233

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6hksa_
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.36.1.1 — PDZ domain

Domain ID domain_id	d6hksb_
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.36.1.1 — PDZ domain

Domain ID domain_id	d6hksc_
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.36.1.1 — PDZ domain

Domain ID domain_id	d6hksd_
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.36.1.1 — PDZ domain

Domain ID domain_id	d6hkse_
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.36.1.1 — PDZ domain

Domain ID domain_id	d6hksf_
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.36.1.1 — PDZ domain

CATH v4.4 (6 domains)

Domain ID domain_id	6hksA00
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	6hksB00
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	6hksC00
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	6hksD00
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	6hksE00
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	6hksF00
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	46.620 Å
Unit-cell length b length_b	77.430 Å
Unit-cell length c length_c	130.030 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.14 °
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	monoclinic

Resolution resolution	2.194 Å
Low-resolution limit resolution_low	43.343 Å
R factor r_factor	0.1967
R_work r_work	0.1941
R_free r_free	0.2468

Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal peptide

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

Tyrosine-protein phosphatase non-receptor type 3

State in the Current Structure

Other States of the Same Protein in the Database

Protein E6

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

6hks__assembly_1__model_1

6hks__assembly_1__model_1 | I(q)

6hks__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal peptide

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

Tyrosine-protein phosphatase non-receptor type 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

Protein E6

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

6hks__assembly_1__model_1

6hks__assembly_1__model_1 | I(q)

6hks__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)