5RVZ: PDB entry 5RVZ

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z1929757385. Determined by X-ray diffraction at 1.98 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 2
Atoms: 15,394
Mol. weight: 202.99 kDa
Ligands: WGA, TPP, MG
Released: 25 Nov 2020

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

Secondary structure: helices and β-sheets

5RVZ contains 92 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	54-66	13
α-helix	67-70	4
α-helix	87-93	7
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	140-154	15
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	268-272	5	2
β-strand	278-283	6	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	341-347	7
α-helix	359	1
β-strand	360-365	6	2
β-strand	368-369	2	3
β-strand	372-373	2	3
α-helix	374-377	4
α-helix	383-389	7
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	456-457	2
α-helix	458-468	11
α-helix	474-493	20
α-helix	528-538	11
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	619-622	4
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	780-782	3
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	843-850	8
β-strand	858-866	9	7
α-helix	872-883	12
β-strand	888-892	5	7
α-helix	893-894	2
α-helix	903-918	16

Chain B: 46 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	50-52	3
α-helix	54-66	13
α-helix	67-70	4
α-helix	87-93	7
β-strand	100	1	8
β-strand	113	1	8
α-helix	115-126	12
β-strand	130-133	4	9
α-helix	140-155	16
α-helix	160-183	24
α-helix	198-211	14
β-strand	216-220	5	9
α-helix	226-234	9
α-helix	238-245	8
α-helix	262-264	3
β-strand	268-271	4	9
α-helix	278	1
β-strand	279-283	5	9
α-helix	284-285	2
α-helix	293-307	15
α-helix	311-313	3
β-strand	325-332	8	9
α-helix	333-338	6
α-helix	341-348	8
β-strand	360-365	6	9
β-strand	368-369	2	10
β-strand	372-373	2	10
α-helix	374-377	4
α-helix	383-390	8
β-strand	393-398	6	9
α-helix	402-419	18
β-strand	423-428	6	9
α-helix	441-443	3
α-helix	446-453	8
α-helix	458-468	11
α-helix	474-493	20
α-helix	528-537	10
α-helix	549-551	3
α-helix	552-556	5
α-helix	557-565	9
β-strand	569	1	11
α-helix	571-584	14
β-strand	588-593	6	12
β-strand	608-609	2	13
β-strand	616-617	2	13
α-helix	619-622	4
β-strand	631-635	5	12
α-helix	641-651	11
β-strand	657-662	6	12
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	12
α-helix	713-719	7
β-strand	735-737	3	12
α-helix	742-754	13
β-strand	761-765	5	12
α-helix	768-770	3
β-strand	777	1	11
α-helix	779-782	4
β-strand	791-792	2	14
α-helix	799-801	3
β-strand	804-808	5	14
α-helix	812-821	10
α-helix	824-829	6
β-strand	830-835	6	14
β-strand	837-839	3	12
α-helix	843-851	9
β-strand	858-866	9	14
α-helix	872-883	12
β-strand	888-892	5	14
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

>5RVZ_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
WGA	(3S)-1-(3-fluoropyridin-2-yl)-4,4-dimethylpyrrolidin-3-ol	C11 H15 F N2 O	1
TPP	Thiamine diphosphate	C12 H19 N4 O7 P2 S	2
MG	Magnesium ion	Mg	3

Primary citation

PanDDA analysis group deposition. 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:

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)
6U3J 2.25 Å, Structure of the 2-oxoadipate dehydrogenase DHTKD1
9WVX 2.8 Å, CryoEM structure of MRGPRX2 with peptide agonist DKD2

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