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- PDB-2w0x: FACTOR INHIBITING HIF-1 ALPHA WITH PYRIDINE 2,4 DICARBOXYLIC ACID -

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Basic information

Entry
Database: PDB / ID: 2w0x
TitleFACTOR INHIBITING HIF-1 ALPHA WITH PYRIDINE 2,4 DICARBOXYLIC ACID
ComponentsHYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR
KeywordsOXIDOREDUCTASE / HYDROXYLASE / DIOXYGENASE / TRANSCRIPTION / TRANSCRIPTION ACTIVATOR/INHIBITOR / HYPOXIA
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 / oxygen sensor activity ...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 / oxygen sensor activity / Notch binding / 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 / cytoplasm / cytosol
Similarity search - Function
Clavaminate synthase-like / 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. / Jelly Rolls / 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 / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / 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
: / PYRIDINE-2,4-DICARBOXYLIC ACID / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsConejo-Garcia, A. / Lienard, B.M.R. / Clifton, I.J. / McDonough, M.A. / Schofield, C.J.
Citation
Journal: Bioorg. Med. Chem. Lett. / Year: 2010
Title: Structural basis for binding of cyclic 2-oxoglutarate analogues to factor-inhibiting hypoxia-inducible factor.
Authors: Conejo-Garcia, A. / McDonough, M.A. / Loenarz, C. / McNeill, L.A. / Hewitson, K.S. / Ge, W. / Lienard, B.M. / Schofield, C.J. / Clifton, I.J.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1 Alpha.
Authors: Elkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Seibel, J.F. / Schlemminger, I. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
History
DepositionOct 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9327
Polymers40,3281
Non-polymers6036
Water3,603200
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)81,86314
Polymers80,6572
Non-polymers1,20612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5900 Å2
ΔGint-145.9 kcal/mol
Surface area31680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.471, 86.471, 147.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR / HYPOXIA-INDUCIBLE FACTOR ASPARAGINE HYDROXYLASE / FACTOR INHIBITING HIF-1 / FIH-1


Mass: 40328.281 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 206 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPYRIDINE-2,4-DICARBOXYLIC ACID(PD2): PUBCHEM CID 10365

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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: 3.43 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 7.5
Details: 1.6M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 5% PEG400, 1MM FESO4, 2MM SUBSTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2005 / Details: RH COATED MIRROR
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.13→61.2 Å / Num. obs: 32255 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 39.71 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 2.12→2.24 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2N

1h2n


Resolution: 2.12→38.67 Å / SU ML: 0.34 / σ(F): 0.03 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 1516 5 %
Rwork0.21 --
obs0.213 30050 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.63 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 50.43 Å2
Baniso -1Baniso -2Baniso -3
1--3.8936 Å2-0 Å20 Å2
2---3.8936 Å2-0 Å2
3---7.7871 Å2
Refinement stepCycle: LAST / Resolution: 2.12→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 34 200 3036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d02919
X-RAY DIFFRACTIONf_angle_d13965
X-RAY DIFFRACTIONf_dihedral_angle_d191076
X-RAY DIFFRACTIONf_chiral_restr0.07395
X-RAY DIFFRACTIONf_plane_restr0525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.125-2.19360.37631120.31382192X-RAY DIFFRACTION80
2.1936-2.2720.31521370.26492364X-RAY DIFFRACTION87
2.272-2.3630.27851320.24242387X-RAY DIFFRACTION88
2.363-2.47050.34241470.23562537X-RAY DIFFRACTION93
2.4705-2.60070.30751480.24372530X-RAY DIFFRACTION93
2.6007-2.76360.30431240.23382604X-RAY DIFFRACTION94
2.7636-2.97690.27091290.2372647X-RAY DIFFRACTION95
2.9769-3.27640.24961270.22992727X-RAY DIFFRACTION97
3.2764-3.75010.23771430.20252757X-RAY DIFFRACTION99
3.7501-4.72340.23361680.16432800X-RAY DIFFRACTION99
4.7234-38.67760.22611490.18322989X-RAY DIFFRACTION99

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