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- PDB-3kcy: Factor inhibiting HIF-1 alpha in complex with 8-hydroxyquinoline -

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Basic information

Entry
Database: PDB / ID: 3kcy
TitleFactor inhibiting HIF-1 alpha in complex with 8-hydroxyquinoline
ComponentsHypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE / hypoxia / HIF-1 / FIH-1 / inhibitor / Dioxygenase / Iron / Metal-binding / Nucleus / Transcription / Transcription regulation
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 / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / Notch binding ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / Notch binding / oxygen sensor activity / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / Jelly Rolls / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Helix Hairpins ...Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / Jelly Rolls / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / quinolin-8-ol / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMoon, H. / Han, S. / Choe, J.
CitationJournal: Mol.Cells / Year: 2010
Title: Crystal structures of human FIH-1 in complex with quinol family inhibitors
Authors: Moon, H. / Han, S. / Park, H. / Choe, J.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)39,5465
Polymers39,1531
Non-polymers3934
Water1,06359
1
A: Hypoxia-inducible factor 1-alpha inhibitor
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)79,09210
Polymers78,3062
Non-polymers7868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area3850 Å2
ΔGint-74 kcal/mol
Surface area30810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.912, 86.912, 144.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

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Components

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


Mass: 39153.016 Da / Num. of mol.: 1 / Fragment: residues 15-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HQY / quinolin-8-ol / 8-hydroxyquinoline


Mass: 145.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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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: 3.49 Å3/Da / Density % sol: 64.72 % / Mosaicity: 1.012 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M ammonium sulfate, 2% polyethyleneglycol 400, 0.1M Tris-HCl, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 10, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→42.14 Å / Num. obs: 25332 / % possible obs: 98.4 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.074 / Χ2: 1.263 / Net I/σ(I): 23.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.384.80.66522561.086190
2.38-2.485.90.43524091.136195.3
2.48-2.597.60.38824951.225199.4
2.59-2.7310.70.33325421.3171100
2.73-2.911.40.2125331.4561100
2.9-3.1211.50.13825591.5071100
3.12-3.4311.90.10125581.4331100
3.43-3.9312.80.08425861.4161100
3.93-4.9513.50.0726091.19199.4
4.95-30130.05727850.776199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→42.14 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.194 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.55 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.335 834 5.1 %RANDOM
Rwork0.255 ---
obs0.259 16313 91.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 132.18 Å2 / Biso mean: 64.296 Å2 / Biso min: 22.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.59→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 22 59 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222790
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.9543799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16924.626147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.6715433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2851514
X-RAY DIFFRACTIONr_chiral_restr0.1090.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022220
X-RAY DIFFRACTIONr_nbd_refined0.2610.21285
X-RAY DIFFRACTIONr_nbtor_refined0.3240.21842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2125
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.27
X-RAY DIFFRACTIONr_mcbond_it0.9191.51696
X-RAY DIFFRACTIONr_mcangle_it1.57222676
X-RAY DIFFRACTIONr_scbond_it1.86531274
X-RAY DIFFRACTIONr_scangle_it2.8744.51123
LS refinement shellResolution: 2.592→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.609 61 -
Rwork0.489 1008 -
all-1069 -
obs--83.71 %

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