6SY1: Human 2-oxoadipate dehydrogenase DHTKD1

Crystal structure of the human 2-oxoadipate dehydrogenase DHTKD1 (E1). Determined by X-ray diffraction at 1.87 Å resolution. Released 24 Jun 2020.

Method: X-ray diffraction
Resolution: 1.87 Å
Organism: Homo sapiens
Chains: 2
Atoms: 14,452
Mol. weight: 202.78 kDa
Ligands: MG, TPP
Released: 24 Jun 2020

Explore 6SY1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SY1 contains 94 α-helices and 54 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 46 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	54-66	13
α-helix	67-70	4
α-helix	87-94	8
β-strand	100-101	2	1
β-strand	112-113	2	1
α-helix	115-126	12
β-strand	130-133	4	2
α-helix	140-155	16
α-helix	160-183	24
α-helix	198-212	15
β-strand	216-220	5	2
α-helix	226-232	7
α-helix	238-245	8
α-helix	262-264	3
β-strand	268-271	4	2
β-strand	279-283	5	2
α-helix	284-285	2
α-helix	293-308	16
α-helix	311-313	3
β-strand	325-332	8	2
α-helix	333-338	6
α-helix	341-348	8
β-strand	359-365	7	2
β-strand	368-369	2	3
β-strand	372-373	2	3
α-helix	374-376	3
α-helix	383-390	8
β-strand	393-398	6	2
α-helix	402-419	18
β-strand	423-428	6	2
α-helix	441-443	3
α-helix	446-454	9
α-helix	458-468	11
α-helix	474-493	20
α-helix	495-497	3
α-helix	500-502	3
α-helix	528-537	10
α-helix	549-551	3
α-helix	552-556	5
α-helix	557-565	9
β-strand	569	1	4
α-helix	571-584	14
β-strand	588-593	6	5
β-strand	608-609	2	6
β-strand	616-617	2	6
α-helix	619-621	3
β-strand	631-635	5	5
α-helix	641-653	13
β-strand	657-662	6	5
α-helix	666-672	7
α-helix	673-675	3
α-helix	676-680	5
α-helix	683-687	5
β-strand	694-698	5	5
α-helix	713-719	7
β-strand	735-737	3	5
α-helix	742-754	13
β-strand	761-765	5	5
α-helix	768-770	3
β-strand	777	1	4
α-helix	779-782	4
β-strand	791-792	2	7
α-helix	799-801	3
β-strand	804-808	5	7
α-helix	812-821	10
α-helix	824-829	6
β-strand	830-835	6	7
β-strand	837-839	3	5
α-helix	843-851	9
β-strand	858-866	9	7
α-helix	872-883	12
β-strand	888-892	5	7
α-helix	893-894	2
α-helix	903-917	15

Chain B: 48 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	54-66	13
α-helix	67-70	4
α-helix	87-95	9
α-helix	115-126	12
β-strand	130-133	4	8
α-helix	140-155	16
α-helix	156-159	4
α-helix	160-183	24
α-helix	198-211	14
β-strand	216-220	5	8
α-helix	226-232	7
α-helix	238-245	8
α-helix	262-264	3
β-strand	268-271	4	8
α-helix	277-278	2
β-strand	279-283	5	8
α-helix	284-285	2
α-helix	293-307	15
α-helix	311-313	3
β-strand	325-332	8	8
α-helix	333-338	6
α-helix	341-347	7
β-strand	359-365	7	8
β-strand	368-369	2	9
β-strand	372-373	2	9
α-helix	374-376	3
α-helix	383-390	8
β-strand	393-398	6	8
α-helix	402-419	18
β-strand	423-428	6	8
α-helix	441-443	3
α-helix	446-454	9
α-helix	458-468	11
α-helix	474-493	20
α-helix	494-496	3
α-helix	519-520	2
α-helix	528-537	10
α-helix	549-551	3
α-helix	552-556	5
α-helix	557-565	9
β-strand	569	1	10
α-helix	571-584	14
β-strand	588-593	6	11
β-strand	608-609	2	12
β-strand	616-617	2	12
α-helix	619-622	4
β-strand	631-635	5	11
α-helix	641-651	11
β-strand	657-662	6	11
α-helix	666-672	7
α-helix	673-675	3
α-helix	676-680	5
α-helix	683-687	5
β-strand	694-698	5	11
α-helix	713-719	7
β-strand	735-737	3	11
α-helix	742-754	13
β-strand	761-765	5	11
α-helix	768-770	3
β-strand	777	1	10
α-helix	779-782	4
β-strand	791-792	2	13
α-helix	799-801	3
β-strand	804-808	5	13
α-helix	812-821	10
α-helix	824-829	6
β-strand	830-835	6	13
β-strand	837-839	3	11
α-helix	843-851	9
β-strand	858-866	9	13
α-helix	872-883	12
β-strand	888-892	5	13
α-helix	893-894	2
α-helix	903-917	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial	A, B	protein	898	Homo sapiens	Q96HY7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6SY1_1 Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial (chains A, B)
MHHHHHHSSGVDLGTENLYFQSMGALERPPVDHGLARLVTVYCEHGHKAAKINPLFTGQA
LLENVPEIQALVQTLQGPFHTAGLLNMGKEEASLEEVLVYLNQIYCGQISIETSQLQSQD
EKDWFAKRFEELQKETFTTEERKHLSKLMLESQEFDHFLATKFSTVKRYGGEGAESMMGF
FHELLKMSAYSGITDVIIGMPHRGRLNLLTGLLQFPPELMFRKMRGLSEFPENFSATGDV
LSHLTSSVDLYFGAHHPLHVTMLPNPSHLEAVNPVAVGKTRGRQQSRQDGDYSPDNSAQP
GDRVICLQVHGDASFCGQGIVPETFTLSNLPHFRIGGSVHLIVNNQLGYTTPAERGRSSL
YCSDIGKLVGCAIIHVNGDSPEEVVRATRLAFEYQRQFRKDVIIDLLCYRQWGHNELDEP
FYTNPIMYKIIRARKSIPDTYAEHLIAGGLMTQEEVSEIKSSYYAKLNDHLNNMAHYRPP
ALNLQAHWQGLAQPEAQITTWSTGVPLDLLRFVGMKSVEVPRELQMHSHLLKTHVQSRME
KMMDGIKLDWATAEALALGSLLAQGFNVRLSGQDVGRGTFSQRHAIVVCQETDDTYIPLN
HMDPNQKGFLEVSNSPLSEEAVLGFEYGMSIESPKLLPLWEAQFGDFFNGAQIIFDTFIS
GGEAKWLLQSGIVILLPHGYDGAGPDHSSCRIERFLQMCDSAEEGVDGDTVNMFVVHPTT
PAQYFHLLRRQMVRNFRKPLIVASPKMLLRLPAAVSTLQEMAPGTTFNPVIGDSSVDPKK
VKTLVFCSGKHFYSLVKQRESLGAKKHDFAIIRVEELCPFPLDSLQQEMSKYKHVKDHIW
SQEEPQNMGPWSFVSPRFEKQLACKLRLVGRPPLPVPAVGIGTVHLHQHEDILAKTFA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
TPP	Thiamine diphosphate	C12 H19 N4 O7 P2 S	2

Primary citation

Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism. Bezerra, G.A., Foster, W.R., Bailey, H.J. et al. IUCrJ (2020) 7:693-706. DOI 10.1107/S205225252000696X · PubMed

Other PDB entries of the same protein (UniProt Q96HY7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5RW1 1.52 Å, PanDDA analysis group deposition of ground-state model of DHTKD1
5RVY 1.61 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z437516460
5RVW 1.61 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with…
5RVX 1.66 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z804566442
5RW0 1.67 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with…
5RVZ 1.98 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with…
6U3J 2.25 Å, Structure of the 2-oxoadipate dehydrogenase DHTKD1
9WVX 2.8 Å, CryoEM structure of MRGPRX2 with peptide agonist DKD2

Browse structure collections

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