5RW1: PDB entry 5RW1

PanDDA analysis group deposition of ground-state model of DHTKD1. Determined by X-ray diffraction at 1.52 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 1.52 Å
Organism: Homo sapiens
Chains: 2
Atoms: 15,406
Mol. weight: 202.78 kDa
Ligands: TPP, MG
Released: 25 Nov 2020

Explore 5RW1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5RW1 contains 95 α-helices and 56 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	33-45	13
α-helix	46-49	4
α-helix	66-72	7
β-strand	79-80	2	1
β-strand	91-92	2	1
α-helix	94-105	12
β-strand	109-112	4	2
α-helix	119-134	16
α-helix	139-162	24
α-helix	177-191	15
β-strand	195-199	5	2
α-helix	205-211	7
α-helix	217-224	8
α-helix	241-243	3
β-strand	247-251	5	2
β-strand	257-262	6	2
α-helix	263-264	2
α-helix	272-286	15
α-helix	290-292	3
β-strand	304-311	8	2
α-helix	312-317	6
α-helix	320-327	8
β-strand	338-344	7	2
β-strand	347-348	2	3
β-strand	351-352	2	3
α-helix	353-355	3
α-helix	362-369	8
β-strand	372-377	6	2
α-helix	381-398	18
β-strand	402-407	6	2
α-helix	420-422	3
α-helix	425-433	9
α-helix	435-436	2
α-helix	437-447	11
α-helix	453-472	20
α-helix	507-516	10
α-helix	528-530	3
α-helix	531-535	5
α-helix	536-544	9
β-strand	548	1	4
α-helix	550-563	14
β-strand	567-572	6	5
β-strand	587-588	2	6
β-strand	595-596	2	6
α-helix	598-601	4
β-strand	610-614	5	5
α-helix	620-632	13
β-strand	636-641	6	5
α-helix	645-651	7
α-helix	652-654	3
α-helix	655-659	5
α-helix	662-666	5
β-strand	673-677	5	5
α-helix	692-698	7
β-strand	714-716	3	5
α-helix	721-733	13
β-strand	740-744	5	5
α-helix	747-749	3
β-strand	756	1	4
α-helix	758-761	4
β-strand	770-771	2	7
α-helix	778-780	3
β-strand	783-787	5	7
α-helix	791-800	10
α-helix	803-808	6
β-strand	809-814	6	7
β-strand	816-818	3	5
α-helix	822-829	8
α-helix	830-832	3
β-strand	837-845	9	7
α-helix	851-862	12
β-strand	867-871	5	7
α-helix	872-873	2
α-helix	882-896	15

Chain B: 49 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
α-helix	33-45	13
α-helix	46-49	4
α-helix	66-72	7
β-strand	79	1	8
β-strand	92	1	8
α-helix	94-105	12
β-strand	109-112	4	9
α-helix	119-134	16
α-helix	139-162	24
α-helix	177-191	15
β-strand	195-199	5	9
α-helix	205-212	8
α-helix	217-224	8
α-helix	241-243	3
β-strand	247-251	5	9
β-strand	257-262	6	9
α-helix	263-264	2
α-helix	272-286	15
α-helix	290-292	3
β-strand	304-311	8	9
α-helix	312-317	6
α-helix	320-327	8
β-strand	339-344	6	9
β-strand	347-348	2	10
β-strand	351-352	2	10
α-helix	353-355	3
α-helix	362-369	8
β-strand	372-377	6	9
α-helix	381-398	18
β-strand	402-407	6	9
α-helix	420-422	3
α-helix	425-433	9
α-helix	435-436	2
α-helix	437-447	11
α-helix	453-472	20
α-helix	474-476	3
α-helix	498-499	2
α-helix	507-516	10
α-helix	528-530	3
α-helix	531-535	5
α-helix	536-544	9
β-strand	548	1	11
α-helix	550-563	14
β-strand	567-572	6	12
β-strand	587-588	2	13
β-strand	595-596	2	13
α-helix	598-601	4
β-strand	610-614	5	12
α-helix	620-632	13
β-strand	636-641	6	12
α-helix	645-651	7
α-helix	652-654	3
α-helix	655-659	5
α-helix	662-666	5
β-strand	673-677	5	12
α-helix	692-698	7
β-strand	714-716	3	12
α-helix	721-733	13
β-strand	740-744	5	12
α-helix	747-749	3
β-strand	756	1	11
α-helix	758-761	4
β-strand	770-771	2	14
α-helix	778-780	3
β-strand	783-787	5	14
α-helix	791-800	10
α-helix	803-808	6
β-strand	809-814	6	14
β-strand	816-818	3	12
α-helix	822-829	8
β-strand	837-845	9	14
α-helix	851-862	12
α-helix	866	1
β-strand	867-871	5	14
α-helix	872-873	2
α-helix	882-896	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

>5RW1_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
TPP	Thiamine diphosphate	C12 H19 N4 O7 P2 S	2
MG	Magnesium ion	Mg	3

Primary citation

PanDDA analysis group deposition of ground-state model. Bezerra, G.A., Foster, W.R., Bailey, H.J. et al. To be published.

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

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…
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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