SAXSdb — 9ngj

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

ATP-binding cassette sub-family D member 3

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–659 Chain B； UniProt 1–659	Not recorded	A1CAN S-{(3R,5S,9S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (3S,7R,11R)-3,7,11,15-tetramethylhexadecanethioate (non-preferred name) × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.13 Å

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 9NGJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8Z0F Cryo-EM structure of ATP-bound human very long-chain fatty acid ABC transporter ABCD3 Deposited 2024-04-09	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 50–659（610 aa） Chain B 50–659（610 aa）	Mutation：E596Q Mutation：E596Q	ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
8Z9X Cryo-EM structure of Phytanoyl-CoA-bound human very long-chain fatty acid ABC transporter ABCD3 Deposited 2024-04-23	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 50–659（610 aa） Chain B 50–659（610 aa）	Not recorded	A1L1A phytanoyl-CoA × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9NGM CryoEM structure of human ABCD3 Deposited 2025-02-22	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–659（659 aa） Chain B 1–659（659 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9W62 Cryo-EM structure of human ABCD3 in inward-facing conformation in the presence of phytanoyl-CoA Deposited 2025-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–659（659 aa）	Not recorded	CLR CHOLESTEROL × 4 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
9W63 Cryo-EM structure of C20:5-CoA bound state human ABCD3 in inward-facing conformation Deposited 2025-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–659（659 aa）	Not recorded	3IX S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate × 2 CLR CHOLESTEROL × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
9W64 Cryo-EM structure of CHS bound state human ABCD3 in inward-facing conformation Deposited 2025-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–659（659 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.81 Å
9W65 Cryo-EM structure of ATP bound state human ABCD3 in inward-facing conformation Deposited 2025-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–659（659 aa）	Mutation：E596Q	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 CLR CHOLESTEROL × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
9W66 Cryo-EM structure of ATP bound state human ABCD3 in outward-facing conformation Deposited 2025-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–659（659 aa）	Mutation：E596Q	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 CLR CHOLESTEROL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

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

View Construct and Data Evidence

UniProt name	ABCD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–659； UniProt 1–659 Author chain B； PDBConstruct 1–659； UniProt 1–659

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	9ngj
Deposition date deposition_date	2025-02-22
Structure title title	CryoEM structure of human ABCD3 bound to Phytanoyl-CoA
Keywords keywords	ABC transporter, Peroxisome, Fatty-acid transport, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	40.48 Å
Radius of gyration Rg (electron density) rg_electron	40.10 Å
Forward intensity I(0) i0	259500000.00
Molecular weight molecular_weight	136720.0 kDa
Excluded volume excluded_volume	173590 Å³
Envelope volume envelope_volume	246680 Å³
Hydration-shell volume shell_volume	52200 Å³
Envelope diameter envelope_diameter	131.4 Å
Shell Rg shell_rg	45.55 Å
Envelope Rg envelope_rg	38.35 Å
Shape Rg shape_rg	40.09 Å
Total Rg total_rg	40.46 Å
Total atoms total_atoms	19392
Residues n_residues	1172
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	132.5 Å
Rg (real space) rg_real	40.43 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	2.5950e+08
I(0) uncertainty (real space) i0_real_error	4.5050e+06
Rg (reciprocal space) rg_reciprocal	40.48 Å
I(0) (reciprocal space) i0_reciprocal	259500000.0000
Solution quality estimate total_estimate	0.8995
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.4 Å
Skewness Skewness skewness	0.195
Kurtosis Kurtosis kurtosis	-0.554
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26720000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.933

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	ATP-binding cassette sub-family D member 3
Molecular weight formula_weight	78243.7 kDa
EC 编号 ec_number	3.1.2.-,7.6.2.-
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	19392

MAAFSKYLTARNSSLAGAAFLLLCLLHKRRRALGLHGKKSGKPPLQNNEKEGKKERAVVDKVFFSRLIQILKIMVPRTFCKETGYLVLIAVMLVSRTYCDVWMIQNGTLIESGIIGRSRKDFKRYLLNFIAAMPLISLVNNFLKYGLNELKLCFRVRLTKYLYEEYLQAFTYYKMGNLDNRIANPDQLLTQDVEKFCNSVVDLYSNLSKPFLDIVLYIFKLTSAIGAQGPASMMAYLVVSGLFLTRLRRPIGKMTITEQKYEGEYRYVNSRLITNSEEIAFYNGNKREKQTVHSVFRKLVEHLHNFILFRFSMGFIDSIIAKYLATVVGYLVVSRPFLDLSHPRHLKSTHSELLEDYYQSGRMLLRMSQALGRIVLAGREMTRLAGFTARITELMQVLKDLNHGKYERTMVSQQEKGIEGVQVIPLIPGAGEIIIADNIIKFDHVPLATPNGDVLIRDLNFEVRSGANVLICGPNGCGKSSLFRVLGELWPLFGGRLTKPERGKLFYVPQRPYMTLGTLRDQVIYPDGREDQKRKGISDLVLKEYLDNVQLGHILEREGGWDSVQDWMDVLSGGEKQRMAMARLFYHKPQFAILDECTSAVSVDVEGYIYSHCRKVGITLFTVSHRKSLWKHHEYYLHMDGRGNYEFKQITEDTVEFGSGSGLVPRGSGGGGSGGGGSGGHHHHHHHH

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	;S-{(3R,5S,9S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (3S,7R,11R)-3,7,11,15-tetramethylhexadecanethioate (non-preferred name) ;
Molecular weight formula_weight	1062.0 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.130 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.13 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	283849

fit	/app/data/saxs_computation/ng/9ngj/9ngj.fit
pddf	/app/data/pr_computation/ng/9ngj/9ngj.pr.out
profile	/app/data/saxs_computation/ng/9ngj/9ngj.dat

CryoEM structure of human ABCD3 bound to Phytanoyl-CoA

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

ATP-binding cassette sub-family D member 3

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)