7BMJ: Aspartyl/asparaginyl beta-hydroxylase

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 5-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39mer-4Ser). Determined by X-ray diffraction at 1.75 Å resolution. Released 2 Jun 2021.

Method
X-ray diffraction
Resolution
1.75 Å
Organism
Homo sapiens
Chains
3
Atoms
7,546
Mol. weight
103.48 kDa
Ligands
MN, U4Q
Released
2 Jun 2021

Explore 7BMJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BMJ contains 42 α-helices and 34 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: 22 helices, 18 β-strands

ElementResiduesLengthSheet
α-helix336-3394
α-helix342-35312
α-helix357-37014
α-helix375-39218
α-helix395-40915
α-helix416-43318
α-helix436-44914
α-helix454-46613
α-helix470-48314
α-helix488-50013
α-helix504-51714
α-helix525-53713
α-helix543-55210
β-strand56111
β-strand56512
β-strand575-57623
α-helix578-5814
α-helix584-5929
α-helix594-60714
β-strand613-61423
α-helix6151
β-strand620-62234
β-strand625-63283
β-strand635-63623
α-helix638-6436
α-helix645-6517
α-helix655-6584
β-strand664-67073
β-strand674-67964
β-strand68312
β-strand686-69493
β-strand700-70454
β-strand707-70934
β-strand71313
β-strand716-71943
β-strand72311
β-strand725-72954
β-strand735-74393
α-helix749-7546
α-helix756-7572
Chain C: 20 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix336-3405
α-helix342-35413
α-helix357-37014
α-helix375-39218
α-helix395-40915
α-helix416-43318
α-helix436-44914
α-helix454-46613
α-helix470-48314
α-helix488-50013
α-helix504-51714
α-helix525-53713
α-helix543-55210
β-strand56115
β-strand57516
α-helix578-5814
α-helix584-5929
α-helix594-60714
β-strand613-61426
β-strand620-62237
β-strand625-63286
β-strand635-63626
α-helix638-6436
α-helix645-6517
α-helix655-6584
β-strand664-67076
β-strand674-67967
β-strand686-69496
β-strand700-70457
β-strand707-70937
β-strand71316
β-strand716-71946
β-strand72315
β-strand725-72957
β-strand735-74396
α-helix749-7546

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Aspartyl/asparaginyl beta-hydroxylaseA, Cprotein429Homo sapiensQ12797 (AlphaFold model)
Coagulation factor XBprotein39Homo sapiensP00742 (AlphaFold model)
Sequence of entity 1 (A, C), FASTA
>7BMJ_1 Aspartyl/asparaginyl beta-hydroxylase (chains A, C)
KPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLA
EKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQL
FPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIP
YLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNG
LKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFT
LWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLRM
HLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTP
QQRRSLPAI
Sequence of entity 2 (B), FASTA
>7BMJ_2 Coagulation factor X (chains B)
DGDQSETSPSQNQGKCKDGLGEYTCTSLEGFEGKNSELF

Ligands and cofactors

IDNameFormulaCopies
MNManganese (II) ionMn2
U4Q5-fluoranylpyridine-2,4-dicarboxylic acidC7 H4 F N O42

Primary citation

Fluorinated derivatives of pyridine-2,4-dicarboxylate are potent inhibitors of human 2-oxoglutarate dependent oxygenases. Brewitz, L., Nakashima, Y., Tumber, A. et al. J Fluor Chem (2021) 247:109804. DOI 10.1016/j.jfluchem.2021.109804

Other PDB entries of the same protein (UniProt Q12797 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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