5RVX: PDB entry 5RVX

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z804566442. Determined by X-ray diffraction at 1.66 Å resolution. Released 25 Nov 2020.

Method
X-ray diffraction
Resolution
1.66 Å
Organism
Homo sapiens
Chains
2
Atoms
15,404
Mol. weight
203.27 kDa
Ligands
MG, TPP, B0Y
Released
25 Nov 2020

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

Secondary structure: helices and β-sheets

5RVX 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

ElementResiduesLengthSheet
α-helix54-6613
α-helix67-704
α-helix87-937
β-strand100-10121
β-strand112-11321
α-helix115-12612
β-strand130-13342
α-helix140-15415
α-helix160-18324
α-helix198-21215
β-strand216-22052
α-helix226-2327
α-helix238-2458
α-helix262-2643
β-strand268-27252
β-strand278-28362
α-helix284-2852
α-helix293-30715
α-helix311-3133
β-strand325-33282
α-helix333-3386
α-helix341-3488
β-strand359-36572
β-strand368-36923
β-strand372-37323
α-helix374-3763
α-helix383-3908
β-strand393-39862
α-helix402-41918
β-strand423-42862
α-helix441-4433
α-helix446-4549
α-helix456-4572
α-helix458-46811
α-helix474-49421
α-helix528-53710
α-helix549-5513
α-helix552-5565
α-helix557-5659
β-strand56914
α-helix571-58414
β-strand588-59365
β-strand608-60926
β-strand616-61726
α-helix619-6224
β-strand631-63555
α-helix641-65313
β-strand657-66265
α-helix666-6727
α-helix673-6753
α-helix676-6805
α-helix683-6875
β-strand694-69855
α-helix713-7197
β-strand735-73735
α-helix742-75413
β-strand761-76555
α-helix768-7703
β-strand77714
α-helix779-7824
β-strand791-79227
α-helix799-8013
β-strand804-80857
α-helix812-82110
α-helix824-8296
β-strand830-83567
β-strand837-83935
α-helix843-8508
α-helix851-8533
β-strand858-86697
α-helix872-88312
β-strand888-89257
α-helix893-8942
α-helix903-91715
Chain B: 46 helices, 28 β-strands
ElementResiduesLengthSheet
α-helix50-523
α-helix54-6613
α-helix67-704
α-helix87-937
β-strand10018
β-strand11318
α-helix115-12612
β-strand130-13349
α-helix140-15516
α-helix160-18324
α-helix198-21215
β-strand216-22059
α-helix226-2327
α-helix238-2458
α-helix262-2643
β-strand268-27149
β-strand279-28359
α-helix284-2852
α-helix293-30715
α-helix311-3133
β-strand325-33289
α-helix333-3386
α-helix341-3488
β-strand359-36579
β-strand368-369210
β-strand372-373210
α-helix374-3763
α-helix383-3908
β-strand393-39869
α-helix402-41918
β-strand423-42869
α-helix441-4433
α-helix446-4549
α-helix458-46811
α-helix474-49320
α-helix519-5202
α-helix528-53710
α-helix549-5513
α-helix552-5565
α-helix557-5659
β-strand569111
α-helix571-58414
β-strand588-593612
β-strand608-609213
β-strand616-617213
α-helix619-6224
β-strand631-635512
α-helix641-65313
β-strand657-662612
α-helix666-6727
α-helix673-6753
α-helix676-6805
α-helix683-6875
β-strand694-698512
α-helix713-7197
β-strand735-737312
α-helix742-75413
β-strand761-765512
α-helix768-7703
β-strand777111
α-helix779-7824
β-strand791-792214
α-helix799-8013
β-strand804-808514
α-helix812-82110
α-helix824-8296
β-strand830-835614
β-strand837-839312
α-helix843-8508
β-strand858-866914
α-helix872-88312
β-strand888-892514
α-helix893-8942
α-helix903-91715

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrialA, Bprotein898Homo sapiensQ96HY7 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>5RVX_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

IDNameFormulaCopies
MGMagnesium ionMg3
TPPThiamine diphosphateC12 H19 N4 O7 P2 S2
B0Y5-ethyl-~{N}-[(1-methylpyrazol-4-yl)methyl]thiophene-2-carboxamideC12 H15 N3 O S2

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:

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