9NGJ | pdb_00009ngj

CryoEM structure of human ABCD3 bound to Phytanoyl-CoA

PDB DOI: https://doi.org/10.2210/pdb9NGJ/pdb
EM Map EMD-49386: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-02-22 Released: 2025-12-17
Deposition Author(s): Gupta, M., Khandelwal, N.K., Stroud, R.M.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9NGJ

This is version 1.0 of the entry. See complete history.

Literature

Structural analysis of a human peroxisomal fatty-acid transporter

Gupta, M., Khandelwal, N.K., Stroud, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 158.61 kDa
Atom Count: 9,618
Modeled Residue Count: 1,172
Deposited Residue Count: 1,376
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family D member 3	A [auth B], B [auth A]	688	Homo sapiens	Mutation(s): 0 Gene Names: ABCD3, PMP70, PXMP1 EC: 3.1.2 (PDB Primary Data), 7.6.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P28288 (Homo sapiens) Explore P28288 Go to UniProtKB: P28288
PHAROS: P28288 GTEx: ENSG00000117528
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28288
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CAN (Subject of Investigation/LOI) Query on A1CAN Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A]	C [auth B], D [auth A]	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) C₄₁ H₇₄ N₇ O₁₇ P₃ S NRJQGHHZMSOUEN-KBMDNNSFSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Khandelwal, N.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.