6U3J: 2-oxoadipate dehydrogenase DHTKD1

Structure of the 2-oxoadipate dehydrogenase DHTKD1. Determined by X-ray diffraction at 2.25 Å resolution. Released 22 Jul 2020.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 2
Atoms: 14,773
Mol. weight: 204.6 kDa
Ligands: MG, TPP
Released: 22 Jul 2020

Explore 6U3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U3J contains 86 α-helices and 60 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: 43 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	1
β-strand	33	1	1
α-helix	54-66	13
α-helix	67-70	4
α-helix	87-93	7
β-strand	100-101	2	2
β-strand	112-113	2	2
α-helix	115-126	12
β-strand	130-133	4	3
α-helix	140-153	14
α-helix	160-183	24
α-helix	198-211	14
β-strand	216-220	5	3
α-helix	226-232	7
α-helix	238-245	8
α-helix	262-264	3
β-strand	267-273	7	3
β-strand	277-283	7	3
α-helix	293-307	15
α-helix	311-313	3
β-strand	325-332	8	3
α-helix	333-338	6
α-helix	341-348	8
β-strand	360-365	6	3
β-strand	368-369	2	4
β-strand	372-373	2	4
α-helix	374-376	3
α-helix	383-389	7
β-strand	393-398	6	3
α-helix	402-419	18
β-strand	423-428	6	3
α-helix	441-443	3
α-helix	446-452	7
α-helix	458-469	12
α-helix	474-493	20
α-helix	514-516	3
α-helix	528-537	10
α-helix	549-550	2
α-helix	551-556	6
α-helix	557-565	9
β-strand	569	1	5
α-helix	571-584	14
β-strand	588-593	6	6
β-strand	608-609	2	7
β-strand	616-617	2	7
α-helix	619-622	4
β-strand	631-635	5	6
α-helix	641-653	13
β-strand	657-662	6	6
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	6
α-helix	713-718	6
β-strand	735-737	3	6
α-helix	742-754	13
β-strand	761-765	5	6
α-helix	768-770	3
β-strand	777	1	5
α-helix	780-782	3
β-strand	791-792	2	8
β-strand	804-808	5	8
α-helix	812-821	10
α-helix	824-829	6
β-strand	830-835	6	8
β-strand	837-839	3	6
α-helix	843-850	8
β-strand	858-866	9	8
α-helix	872-883	12
β-strand	888-892	5	8
α-helix	893-894	2
α-helix	903-917	15

Chain B: 43 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	9
β-strand	33	1	9
α-helix	54-66	13
α-helix	67-70	4
α-helix	87-93	7
β-strand	100-101	2	10
β-strand	112-113	2	10
α-helix	115-126	12
β-strand	130-133	4	11
α-helix	140-153	14
α-helix	160-183	24
α-helix	198-211	14
β-strand	216-220	5	11
α-helix	226-232	7
α-helix	238-245	8
α-helix	262-264	3
β-strand	267-273	7	11
β-strand	277-283	7	11
α-helix	293-307	15
α-helix	311-313	3
β-strand	325-332	8	11
α-helix	333-338	6
α-helix	341-348	8
β-strand	360-365	6	11
β-strand	368-369	2	12
β-strand	372-373	2	12
α-helix	374-376	3
α-helix	383-389	7
β-strand	393-398	6	11
α-helix	402-419	18
β-strand	423-428	6	11
α-helix	441-443	3
α-helix	446-452	7
α-helix	458-469	12
α-helix	474-493	20
α-helix	514-516	3
α-helix	528-537	10
α-helix	549-550	2
α-helix	551-556	6
α-helix	557-565	9
β-strand	569	1	13
α-helix	571-584	14
β-strand	588-593	6	14
β-strand	608-609	2	15
β-strand	616-617	2	15
α-helix	619-622	4
β-strand	631-635	5	14
α-helix	641-653	13
β-strand	657-662	6	14
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	14
α-helix	713-719	7
β-strand	735-737	3	14
α-helix	742-754	13
β-strand	761-765	5	14
α-helix	768-770	3
β-strand	777	1	13
α-helix	780-782	3
β-strand	791-792	2	16
β-strand	804-808	5	16
α-helix	812-821	10
α-helix	824-829	6
β-strand	830-835	6	16
β-strand	837-839	3	14
α-helix	843-850	8
β-strand	858-866	9	16
α-helix	872-883	12
β-strand	888-892	5	16
α-helix	893-894	2
α-helix	903-917	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial	A, B	protein	904	Homo sapiens	Q96HY7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6U3J_1 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial (chains A, B)
MGQTERGVYGYRPRKPESREPQGALERPPVDHGLARLVTVYCEHGHKAAKINPLFTGQAL
LENVPEIQALVQTLQGPFHTAGLLNMGKEEASLEEVLVYLNQIYCGQISIETSQLQSQDE
KDWFAKRFEELQKETFTTEERKHLSKLMLESQEFDHFLATKFSTVKRYGGEGAESMMGFF
HELLKMSAYSGITDVIIGMPHRGRLNLLTGLLQFPPELMFRKMRGLSEFPENFSATGDVL
SHLTSSVDLYFGAHHPLHVTMLPNPSHLEAVNPVAVGKTRGRQQSRQDGDYSPDNSAQPG
DRVICLQVHGDASFCGQGIVPETFTLSNLPHFRIGGSVHLIVNNQLGYTTPAERGRSSLY
CSDIGKLVGCAIIHVNGDSPEEVVRATRLAFEYQRQFRKDVIIDLLCYRQWGHNELDEPF
YTNPIMYKIIRARKSIPDTYAEHLIAGGLMTQEEVSEIKSSYYAKLNDHLNNMAHYRPPA
LNLQAHWQGLAQPEAQITTWSTGVPLDLLRFVGMKSVEVPRELQMHSHLLKTHVQSRMEK
MMDGIKLDWATAEALALGSLLAQGFNVRLSGQDVGRGTFSQRHAIVVCQETDDTYIPLNH
MDPNQKGFLEVSNSPLSEEAVLGFEYGMSIESPKLLPLWEAQFGDFFNGAQIIFDTFISG
GEAKWLLQSGIVILLPHGYDGAGPDHSSCRIERFLQMCDSAEEGVDGDTVNMFVVHPTTP
AQYFHLLRRQMVRNFRKPLIVASPKMLLRLPAAVSTLQEMAPGTTFNPVIGDSSVDPKKV
KTLVFCSGKHFYSLVKQRESLGAKKHDFAIIRVEELCPFPLDSLQQEMSKYKHVKDHIWS
QEEPQNMGPWSFVSPRFEKQLACKLRLVGRPPLPVPAVGIGTVHLHQHEDILAKTFAHHH
HHHH

Ligands and cofactors

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

Primary citation

Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex. Leandro, J., Khamrui, S., Wang, H. et al. ACS Chem Biol (2020) 15:2041-2047. DOI 10.1021/acschembio.0c00114 · 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…
6SY1 1.87 Å, Crystal structure of the human 2-oxoadipate dehydrogenase DHTKD1 (E1)
5RVZ 1.98 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with…
9WVX 2.8 Å, CryoEM structure of MRGPRX2 with peptide agonist DKD2

Browse structure collections

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