SAXSdb — 2dok

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

Telomerase-binding protein EST1A

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1239–1419	Fragment：PIN domain, Residues 6-186	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；278 K；1.26M (NH4)2SO4, 0.1M CHES-NaOH, 0.2M NaCl, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 278.0K	Resolution 1.80 Å R-free 0.254
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1239–1419	Fragment：PIN domain, Residues 6-186	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；278 K；1.26M (NH4)2SO4, 0.1M CHES-NaOH, 0.2M NaCl, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 278.0K	Resolution 1.80 Å R-free 0.254
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1239–1419 Chain B； UniProt 1239–1419	Fragment：PIN domain, Residues 6-186	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；278 K；1.26M (NH4)2SO4, 0.1M CHES-NaOH, 0.2M NaCl, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 278.0K	Resolution 1.80 Å R-free 0.254

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 2DOK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HWW Structure of PIN domain of human SMG6 Deposited 2006-08-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1239–1419（181 aa） Fragment：PIN Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；Jeffamine 2000 32%, 0.1M Hepes pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.80 Å R-free 0.267
2HWW Structure of PIN domain of human SMG6 Deposited 2006-08-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1239–1419（181 aa） Fragment：PIN Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；Jeffamine 2000 32%, 0.1M Hepes pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.80 Å R-free 0.267
2HWW Structure of PIN domain of human SMG6 Deposited 2006-08-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1239–1419（181 aa） Fragment：PIN Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；Jeffamine 2000 32%, 0.1M Hepes pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.80 Å R-free 0.267
2HWX Structure of human SMG6 E1282C PIN domain mutant. Deposited 2006-08-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1239–1419（181 aa） Fragment：PIN domain	Mutation：E1282C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；20% Jeffamine 2000, 0.1M Hepes 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.239
4UM2 Crystal structure of the TPR domain of SMG6 Deposited 2014-05-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 580–1166（587 aa） Fragment：TETRATRICOPEPTIDE REPEAT, RESIDUES 580-1166	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；50MM MES PH 5.5, 200MM AMMONIUM ACETATE, 2.5% 2-METHYL-2,4-PENTANEDIOL	Resolution 2.10 Å R-free 0.237
8RXB Human UPF1 CH domain in complex with SMG6 peptide Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain B 404–418（15 aa） Chain F 404–418（15 aa） Chain G 404–418（15 aa） Chain J 404–418（15 aa） Chain N 404–418（15 aa） Chain Q 404–418（15 aa）	Not recorded	ZN ZINC ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；solution (28% (w/v) PEG 3500, 0.2M Lithium sulfate and 0.1 M Tris pH 7.8)	Resolution 2.60 Å R-free 0.295

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EST1A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–186； UniProt 1239–1419 Author chain B； PDBConstruct 6–186； UniProt 1239–1419

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	2dok
Deposition date deposition_date	2006-05-01
Structure title title	Crystal structure of the PIN domain of human EST1A
Keywords keywords	telomerase-associated protein, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.66 Å
Radius of gyration Rg (electron density) rg_electron	23.67 Å
Forward intensity I(0) i0	23953000.00
Molecular weight molecular_weight	37763.0 kDa
Excluded volume excluded_volume	47614 Å³
Envelope volume envelope_volume	60596 Å³
Hydration-shell volume shell_volume	22061 Å³
Envelope diameter envelope_diameter	80.7 Å
Shell Rg shell_rg	29.69 Å
Envelope Rg envelope_rg	23.82 Å
Shape Rg shape_rg	23.67 Å
Total Rg total_rg	24.45 Å
Total atoms total_atoms	2657
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

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

Maximum dimension Dmax dmax	98.3 Å
Rg (real space) rg_real	24.66 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	2.3950e+07
I(0) uncertainty (real space) i0_real_error	3.6950e+05
Rg (reciprocal space) rg_reciprocal	24.66 Å
I(0) (reciprocal space) i0_reciprocal	23950000.0000
Solution quality estimate total_estimate	0.5437
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.301
Kurtosis Kurtosis kurtosis	-0.530
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5182000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.511; Stabil: 1.000; Sysdev: 0.338; Positv: 1.000; Valcen: 0.518; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2dokA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

Domain ID domain_id	2dokB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

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8. Citations (1)

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Unit-cell length a length_a	107.326 Å
Unit-cell length b length_b	51.586 Å
Unit-cell length c length_c	100.480 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2150
R_work r_work	0.2131
R_free r_free	0.2538

Description description	Telomerase-binding protein EST1A
Molecular weight formula_weight	21110.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2959

Crystal structure of the PIN domain of human EST1A

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

Telomerase-binding protein EST1A

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	302

fit	/app/data/saxs_computation/do/2dok/2dok.fit
pddf	/app/data/pr_computation/do/2dok/2dok.pr.out
profile	/app/data/saxs_computation/do/2dok/2dok.dat