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- PDB-9xs5: Factor inhibiting HIF-1 alpha in complex with Mn(II) and morin -

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Basic information

Entry
Database: PDB / ID: 9xs5
TitleFactor inhibiting HIF-1 alpha in complex with Mn(II) and morin
ComponentsHypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE / Factor inhibiting HIF-1 alpha / Dioxygenase
Function / homology
Function and homology information


hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / regulation of vascular endothelial growth factor receptor signaling pathway / Cellular response to hypoxia / positive regulation of vasculogenesis / carboxylic acid binding / ankyrin repeat binding ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / regulation of vascular endothelial growth factor receptor signaling pathway / Cellular response to hypoxia / positive regulation of vasculogenesis / carboxylic acid binding / ankyrin repeat binding / Notch binding / oxygen sensor activity / negative regulation of Notch signaling pathway / positive regulation of myoblast differentiation / NF-kappaB binding / ferrous iron binding / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA-templated transcription / nucleoplasm / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / Chem-MRI / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsNakashima, Y. / Akhsanitaqwim, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K18295 Japan
Japan Society for the Promotion of Science (JSPS)25K02418 Japan
CitationJournal: J.Nat.Prod. / Year: 2026
Title: Structural Insights into Metal-Chelating Natural Inhibitors of Factor Inhibiting HIF-1 alpha.
Authors: Akhsanitaqwim, Y. / Nakashima, Y. / Ikumi, N. / Morita, H.
History
DepositionNov 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxia-inducible factor 1-alpha inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1668
Polymers40,3281
Non-polymers8377
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.626, 86.626, 148.234
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

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Components

#1: Protein Hypoxia-inducible factor 1-alpha inhibitor / Factor inhibiting HIF-1 / FIH-1 / Hypoxia-inducible factor asparagine hydroxylase


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-MRI / 2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one / Morin


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES-NaOH (pH 7.0), 4% (w/v) PEG 400, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.007 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.33→47.22 Å / Num. obs: 43012 / % possible obs: 95.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 49.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 20.7
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2319 / CC1/2: 0.756 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→47.22 Å / SU ML: 0.3173 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1125
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2518 3687 8.57 %
Rwork0.213 39325 -
obs0.2163 43012 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.1 Å2
Refinement stepCycle: LAST / Resolution: 2.33→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 47 63 2861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372875
X-RAY DIFFRACTIONf_angle_d0.66993918
X-RAY DIFFRACTIONf_chiral_restr0.0456394
X-RAY DIFFRACTIONf_plane_restr0.0053516
X-RAY DIFFRACTIONf_dihedral_angle_d14.7847377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.36231440.33371557X-RAY DIFFRACTION95.4
2.36-2.390.36421430.30761553X-RAY DIFFRACTION95.77
2.39-2.430.26281430.29541531X-RAY DIFFRACTION95.33
2.43-2.460.37131490.28581559X-RAY DIFFRACTION95.37
2.46-2.50.29171380.29641507X-RAY DIFFRACTION94.87
2.5-2.540.30741470.28261539X-RAY DIFFRACTION95.31
2.54-2.590.34041510.26631534X-RAY DIFFRACTION94.88
2.59-2.630.34671400.26211532X-RAY DIFFRACTION94.46
2.63-2.680.26091460.27581546X-RAY DIFFRACTION94.42
2.68-2.740.3151410.26381511X-RAY DIFFRACTION94.45
2.74-2.80.28631480.26661519X-RAY DIFFRACTION94.07
2.8-2.860.3711440.25981541X-RAY DIFFRACTION94.19
2.86-2.940.33071420.27871497X-RAY DIFFRACTION93.55
2.94-3.010.28961420.25311527X-RAY DIFFRACTION93.87
3.02-3.10.25661430.25171516X-RAY DIFFRACTION93.36
3.1-3.20.30131390.25021512X-RAY DIFFRACTION92.7
3.2-3.320.27051430.23861501X-RAY DIFFRACTION93.36
3.32-3.450.25421430.21641499X-RAY DIFFRACTION92.61
3.45-3.610.25041310.20971512X-RAY DIFFRACTION92.46
3.61-3.80.2521400.20171440X-RAY DIFFRACTION89.22
3.8-4.040.22921400.18081469X-RAY DIFFRACTION91.84
4.04-4.350.2171360.16761520X-RAY DIFFRACTION92.77
4.35-4.780.19361430.16231503X-RAY DIFFRACTION92.89
4.79-5.480.21991320.17511482X-RAY DIFFRACTION91.44
5.48-6.90.22561370.20611482X-RAY DIFFRACTION91.73
6.9-47.220.20151420.17291436X-RAY DIFFRACTION88.65

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