Fatty acid coenzyme A (CoA), which is synthesized from fatty acids and CoA, plays an important role in lipid metabolism as it is used for beta oxidation and lipid biosynthesis. Beta oxidation, a metabolic pathway for degrading fatty acid CoA to extract acetyl CoA, occurs at mitochondria and peroxisomes. Beta oxidation in mitochondria plays a vital role in supplying acetyl CoA, FADH2, and NADH to TCA cycle, whereas in peroxisomes plays an important role in the degradation of lipids, including very long chain fatty acid CoA, which cannot be transported to mitochondria. ABCD1, ABCD2, and ABCD3, which belong to the ATP-binding cassette transporters (ABC transporters), transport long chain fatty acid acyl CoA from cytoplasm to peroxisome. ABCD1, 2, and 3 have a difference in the specificity of substrate. ABCD1 and 2 mainly transport saturated long chain fatty acid CoA, whereas ABCD3 transports unsaturated long chain fatty acid CoA and branched fatty acid CoA. Several structures have been reported about ABCD1, but the structure of ABCD3 has not yet been elucidated. We analyzed the structure of ABCD3 to obtain a detailed structural basis for its substrate specificity. As a result, we determined ATP bound ABCD3 structure reconstituted into lipid nanodisc which is similar to natural lipid environment than detergent at 4.5 Å. In the near future, we will acquire the structure of ABCD3 bound to its substrate and will elucidate the molecular basis of substrate specificity among ABCD family, providing insights into diseases caused by abnormal lipid metabolism.