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- PDB-9xs3: Factor inhibiting HIF-1 alpha in complex with Mn(II) and wogonin -

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Basic information

Entry
Database: PDB / ID: 9xs3
TitleFactor inhibiting HIF-1 alpha in complex with Mn(II) and wogonin
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
: / : / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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)41,0527
Polymers40,3281
Non-polymers7236
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.687, 86.687, 148.502
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

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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-A1MCQ / wogonin / 8-methoxy-5,7-bis(oxidanyl)-2-phenyl-chromen-4-one


Mass: 284.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O5 / 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.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES-NaOH (pH 7.0), 2% (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: 1.005 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.6→49.5 Å / Num. obs: 33099 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 59.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.4
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2172 / CC1/2: 0.707 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.27 Å / SU ML: 0.3638 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4328
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 3291 9.94 %
Rwork0.1889 29808 -
obs0.1928 33099 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.48 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 41 58 2832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262853
X-RAY DIFFRACTIONf_angle_d0.5723885
X-RAY DIFFRACTIONf_chiral_restr0.0424389
X-RAY DIFFRACTIONf_plane_restr0.0036512
X-RAY DIFFRACTIONf_dihedral_angle_d18.59941040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.36781380.33591236X-RAY DIFFRACTION99.85
2.64-2.680.33081360.31151256X-RAY DIFFRACTION100
2.68-2.720.31751360.29711260X-RAY DIFFRACTION100
2.72-2.760.31651380.27251236X-RAY DIFFRACTION99.93
2.76-2.810.30051390.26361250X-RAY DIFFRACTION100
2.81-2.860.31311400.25391240X-RAY DIFFRACTION99.78
2.86-2.920.27741370.24921254X-RAY DIFFRACTION99.78
2.92-2.980.26751380.24321252X-RAY DIFFRACTION99.86
2.98-3.040.28091300.22881210X-RAY DIFFRACTION99.85
3.04-3.110.31341400.24581268X-RAY DIFFRACTION99.86
3.11-3.190.26191350.25141237X-RAY DIFFRACTION99.78
3.19-3.280.33311340.24221237X-RAY DIFFRACTION99.78
3.28-3.370.28541440.21331270X-RAY DIFFRACTION99.86
3.37-3.480.2461410.19431231X-RAY DIFFRACTION99.85
3.48-3.60.20161400.19341242X-RAY DIFFRACTION99.07
3.61-3.750.22091330.16341224X-RAY DIFFRACTION98.98
3.75-3.920.20911350.17311252X-RAY DIFFRACTION99.21
3.92-4.130.18041330.15511249X-RAY DIFFRACTION99.07
4.13-4.390.16161330.13921227X-RAY DIFFRACTION98.98
4.39-4.720.16511390.13491220X-RAY DIFFRACTION98.62
4.72-5.20.16561400.13831235X-RAY DIFFRACTION99.71
5.2-5.950.22441410.17791234X-RAY DIFFRACTION99.35
5.95-7.490.28541390.19721243X-RAY DIFFRACTION99.42
7.5-47.270.20561320.17151245X-RAY DIFFRACTION98.99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4028284017250.395729641415-0.1496638988942.772913031822.543450305433.19042976862-0.3650426529810.206120358253-0.3686276980590.972173937812-0.262034125020.417859060530.5624443274880.4060488040870.3802456348990.9616165024810.01549160776520.2577216163510.783665038982-0.09757904354231.158148271554.71638135196-26.566139996724.242919761
22.59003622280.0956686353126-0.6352869614322.35221866841.681105062472.48691683761-0.03839454704060.1131242671650.06705242855730.226342028584-0.02046643616820.456072496129-0.270438882644-0.1467210903910.06285418856310.6748237001040.05953908568670.1331497834140.2832976828980.02344705364220.46910546965918.5300944066-21.316163985516.7321512823
31.43360200583-0.465650297424-0.2895058817171.689069435740.358039929160.6055431984230.3130673913731.01027209691-0.0900315441192-0.953713299864-0.5080844721690.182427204218-0.665839883356-0.4487136539960.1541803008841.088699341570.22085311853-0.05309256854230.790938007160.02880452777140.65163489172713.5144753301-23.8639742911-3.97341112413
42.58454840673-0.535162821965-0.4502473081823.117948002451.563651709412.063702914240.1450770058670.3505561578390.719549959328-0.6269675890810.136477912596-0.608883382147-0.7363922304930.276840850914-0.298560197850.87296245273-0.04982553635240.205363483550.443681317221-5.73769699417E-50.65593154448726.9220604145-12.705368292613.6730663968
51.12090856522-1.37613182442-1.130613583313.175827376281.960929194662.51558937805-0.03180958542980.05161194586990.1005157016980.2096994771140.1145511624190.187442018099-0.08339598277420.0770878301419-0.05042613066370.5140745562820.008706062558110.09647769176330.316347255211-0.002000689054330.43984026588426.1206858745-35.78298537897.91879062847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 190 )
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 349 )

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