SAXSdb — 6iwd

▼

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

Tyrosine-protein phosphatase non-receptor type 14

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 886–1187	Fragment：UNP residues 886-1187	HPV18 E7 × 2 （Q76Z96） CL CHLORIDE ION × 2 PO4 PHOSPHATE ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris-HCl pH 8.0, 25% (w/v) polyethylene glycol 3350, 0.25 M lithium sulfate monohydrate, and 2% (v/v) tert-butanol	Resolution 1.80 Å R-free 0.212

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6IWD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BZL CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE N14 AT 1. 65 A RESOLUTION Deposited 2005-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 886–1187（302 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 886-1187	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；SITTING DROP, 20% PEG3350, 0.2 M LI2SO4, 0.1 M BIS TRIS PROPANE PH 6.5, CRYO 20% ETHYLENE GLYCOL	Resolution 1.65 Å R-free 0.217
6JJW Crystal Structure of KIBRA and PTPN14 complex Deposited 2019-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 428–455（28 aa）	Not recorded	CL CHLORIDE ION × 8 FMT FORMIC ACID × 3 GOL GLYCEROL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；700mM magnesium formate, 100mM Bis-Tris Propane (pH 7.0)	Resolution 2.40 Å R-free 0.242

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTN14_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–303； UniProt 886–1187

HPV18 E7

Human papillomavirus type 18

UniProt Q76Z96

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 54–105	Fragment：UNP residues 54-105	Tyrosine-protein phosphatase non-receptor type 14 × 2 （Q15678） CL CHLORIDE ION × 2 PO4 PHOSPHATE ION × 4 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris-HCl pH 8.0, 25% (w/v) polyethylene glycol 3350, 0.25 M lithium sulfate monohydrate, and 2% (v/v) tert-butanol	Resolution 1.80 Å R-free 0.212

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q76Z96_HPV18
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–55； UniProt 54–105

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6iwd
Deposition date deposition_date	2018-12-05
Structure title title	The PTP domain of human PTPN14 in a complex with the CR3 domain of HPV18 E7
Keywords keywords	ONCOPROTEIN; ONCOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.55 Å
Radius of gyration Rg (electron density) rg_electron	20.58 Å
Forward intensity I(0) i0	26064000.00
Molecular weight molecular_weight	38526.0 kDa
Excluded volume excluded_volume	48005 Å³
Envelope volume envelope_volume	56482 Å³
Hydration-shell volume shell_volume	22850 Å³
Envelope diameter envelope_diameter	75.8 Å
Shell Rg shell_rg	27.30 Å
Envelope Rg envelope_rg	20.98 Å
Shape Rg shape_rg	20.50 Å
Total Rg total_rg	21.67 Å
Total atoms total_atoms	2696
Residues n_residues	338
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.6 Å
Rg (real space) rg_real	21.47 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.6060e+07
I(0) uncertainty (real space) i0_real_error	3.4420e+05
Rg (reciprocal space) rg_reciprocal	21.48 Å
I(0) (reciprocal space) i0_reciprocal	26060000.0000
Solution quality estimate total_estimate	0.7982
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.296
Kurtosis Kurtosis kurtosis	-0.198
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5345000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein phosphatase non-receptor type 14
Molecular weight formula_weight	35063.3 kDa
EC 编号 ec_number	3.1.3.48
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	2968

MVDATRVPMDERFRTLKKKLEEGMVFTEYEQIPKKKANGIFSTAALPENAERSRIREVVPYEENRVELIPTKENNTGYINASHIKVVVGGAEWHYIATQGPLPHTCHDFWQMVWEQGVNVIAMVTAEEEGGRTKSHRYWPKLGSKHSSATYGKFKVTTKFRTDSVCYATTGLKVKHLLSGQERTVWHLQYTDWPDHGCPEDVQGFLSYLEEIQSVRRHTNSMLEGTKNRHPPIVVHCSAGVGRTGVLILSELMIYCLEHNEKVEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQNSRLI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	HPV18 E7
Molecular weight formula_weight	6283.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHMAEPQRHTMLCMCCKCEARIELVVESSADDLRAFQQLFLNTLSFVCPWCASQQ

来源 Source

来源生物 organism	Human papillomavirus type 18
NCBI Class编号 ncbi_taxonomy_id	333761
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	268

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6iwda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6iwdA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

Domain ID domain_id	6iwdB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	330 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	54.573 Å
Unit-cell length b length_b	169.153 Å
Unit-cell length c length_c	42.530 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	29.987 Å
R factor r_factor	0.1873
R_work r_work	0.1858
R_free r_free	0.2125

fit	/app/data/saxs_computation/iw/6iwd/6iwd.fit
pddf	/app/data/pr_computation/iw/6iwd/6iwd.pr.out
profile	/app/data/saxs_computation/iw/6iwd/6iwd.dat

The PTP domain of human PTPN14 in a complex with the CR3 domain of HPV18 E7

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

Tyrosine-protein phosphatase non-receptor type 14

State in the Current Structure

Other States of the Same Protein in the Database

HPV18 E7

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)