SAXSdb — 7dkl

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

DEP domain-containing mTOR-interacting protein

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 21–235	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Ammonium acetate, 24% PEG 3350	Resolution 1.50 Å R-free 0.217

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 7DKL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7OWG human DEPTOR in a complex with mutant human mTORC1 A1459P Deposited 2021-06-18	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: Octameric	Chain O 1–409（409 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES, pH 7.5, 200 mM NaCl, 1 mM TCEP, 1 mM MgCl2, 500 uM AMP-PNP cryo-EM vitrification conditions Cryogen ETHANE；blotting time of 2 s and a force of -15.	Resolution 4.70 Å
7PE7 cryo-EM structure of DEPTOR bound to human mTOR complex 2, overall refinement Deposited 2021-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain I 1–409（409 aa） Chain J 1–409（409 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 2 ACE ACETYL GROUP × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
7PE8 cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one protomer Deposited 2021-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 1–409（409 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ACE ACETYL GROUP × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7PE9 cryo-EM structure of DEPTOR bound to human mTOR complex 2, DEPt-bound subset local refinement Deposited 2021-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 1–409（409 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ACE ACETYL GROUP × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7PEA cryo-EM structure of DEPTOR bound to human mTOR complex 1, overall refinement Deposited 2021-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain I 1–409（409 aa） Chain J 1–409（409 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.07 Å
7PEB cryo-EM structure of DEPTOR bound to human mTOR complex 1, focussed on one protomer Deposited 2021-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 1–409（409 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å
7PEC cryo-EM structure of DEPTOR bound to human mTOR complex 1, DEPt-bound subset local refinement Deposited 2021-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 1–409（409 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.24 Å
7PED DEPTOR DEP domain tandem (DEPt) Deposited 2021-08-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–230（230 aa） Chain B 1–230（230 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；PEG3350,natrium hydrochlorid	Resolution 1.93 Å R-free 0.226

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPTOR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–216； UniProt 21–235

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	7dkl
Deposition date deposition_date	2020-11-24
Structure title title	Crystal structure of the tandem DEP domains of DEPTOR
Keywords keywords	mTOR inhibitor, PA binding protein, DEP domain, ANIONIC LIPID BINDING PROTEIN, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
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	20.57 Å
Radius of gyration Rg (electron density) rg_electron	19.78 Å
Forward intensity I(0) i0	11685300.00
Molecular weight molecular_weight	24941.0 kDa
Excluded volume excluded_volume	30967 Å³
Envelope volume envelope_volume	36936 Å³
Hydration-shell volume shell_volume	16484 Å³
Envelope diameter envelope_diameter	74.4 Å
Shell Rg shell_rg	25.04 Å
Envelope Rg envelope_rg	19.91 Å
Shape Rg shape_rg	19.79 Å
Total Rg total_rg	20.52 Å
Total atoms total_atoms	1755
Residues n_residues	215
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	73.1 Å
Rg (real space) rg_real	20.62 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.1690e+07
I(0) uncertainty (real space) i0_real_error	1.3890e+05
Rg (reciprocal space) rg_reciprocal	20.61 Å
I(0) (reciprocal space) i0_reciprocal	11690000.0000
Solution quality estimate total_estimate	0.8452
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.398
Kurtosis Kurtosis kurtosis	-0.352
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2741000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.705; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.983

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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	7dklA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	7dklA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	39.582 Å
Unit-cell length b length_b	63.582 Å
Unit-cell length c length_c	89.081 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	25.876 Å
R factor r_factor	0.1798
R_work r_work	0.1779
R_free r_free	0.2175

Description description	DEP domain-containing mTOR-interacting protein
Molecular weight formula_weight	26059.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1854

Crystal structure of the tandem DEP domains of DEPTOR

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

DEP domain-containing mTOR-interacting protein

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	99

fit	/app/data/saxs_computation/dk/7dkl/7dkl.fit
pddf	/app/data/pr_computation/dk/7dkl/7dkl.pr.out
profile	/app/data/saxs_computation/dk/7dkl/7dkl.dat