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- PDB-2wa4: FACTOR INHIBITING HIF-1 ALPHA WITH N,3-dihydroxybenzamide -

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Basic information

Entry
Database: PDB / ID: 2wa4
TitleFACTOR INHIBITING HIF-1 ALPHA WITH N,3-dihydroxybenzamide
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 / 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
N,3-DIHYDROXYBENZAMIDE / : / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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-1Alpha
Authors: Elkins, J. / Hewitson, K.S. / McNeill, L. / Seibel, J. / Schlemminger, I. / Pugh, C. / Ratcliffe, P. / Schofield, C.J.
History
DepositionFeb 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: 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

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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)40,7865
Polymers40,3281
Non-polymers4584
Water97354
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)81,57310
Polymers80,6572
Non-polymers9168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3450 Å2
ΔGint-50.6 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.115, 87.115, 150.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

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Components

#1: Protein HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR / FACTOR INHIBITING HIF1 / 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
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-069 / N,3-DIHYDROXYBENZAMIDE


Mass: 153.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN,3-DIHYDROXYBENZAMIDE (069): PUBCHEM CID 24701909

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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: 3.68 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 7.5
Details: 1.5M AMMONIUM SULFATE, 100MM HEPES PH 7.5, 3% PEG400, 1MM FESO4, 28MB/ML PROTEIN, 10MM SUBSTRATE. CRYSTALS ARE DEEP RED.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2004 / 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: 2.49→37.77 Å / Num. obs: 20923 / % possible obs: 99 % / Redundancy: 9.1 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.8
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.8 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2N

1h2n


Resolution: 2.5→75.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 17.271 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26672 1039 5 %RANDOM
Rwork0.21124 ---
obs0.2139 19768 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.511 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→75.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 28 54 2808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222835
X-RAY DIFFRACTIONr_bond_other_d0.0030.021942
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.9553845
X-RAY DIFFRACTIONr_angle_other_deg1.0093.0014699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6265328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65124.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13515457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5211515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
X-RAY DIFFRACTIONr_nbd_refined0.2470.2652
X-RAY DIFFRACTIONr_nbd_other0.2110.21937
X-RAY DIFFRACTIONr_nbtor_refined0.1990.21369
X-RAY DIFFRACTIONr_nbtor_other0.0950.21463
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0460.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0611.51708
X-RAY DIFFRACTIONr_mcbond_other0.2091.5662
X-RAY DIFFRACTIONr_mcangle_it1.7222676
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57931327
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9524.51169
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 81 -
Rwork0.45 1455 -
obs--100 %
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)
14.1262-2.816-1.799520.65258.42223.5479-0.811.4008-0.006-1.36450.52330.4017-1.0970.18240.28670.4962-0.0912-0.20670.5207-0.09480.4834.16326.24312.21
21.10450.5737-0.02843.971.11483.2418-0.1660.22330.0065-0.68240.00390.24310.04750.07730.16210.206-0.0684-0.1465-0.23630.0170.558519.69925.18715.478
33.05270.97471.11064.9641.67261.1550.0813-0.50050.01460.9025-0.2865-0.07370.5336-0.32320.20520.4009-0.13610.0747-0.0360.07230.416717.71122.57840.27
429.05647.013511.02672.17034.767213.4712-0.1909-0.39230.19260.44690.08991.06990.52990.11490.10110.4117-0.21040.16960.0661-0.190.53639.87719.20541.495
53.0993-0.3219-1.89694.23562.37496.39310.0764-0.3364-0.09790.82690.1271-0.20580.92060.1179-0.20340.3466-0.1205-0.1173-0.24480.03140.55119.0613.00427.853
61.11.08080.91032.20661.72121.6623-0.0006-0.0827-0.0562-0.01270.05520.03420.09870.2026-0.05450.1886-0.0255-0.0732-0.0938-0.00010.576526.37234.40429.145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 30
2X-RAY DIFFRACTION2A31 - 79
3X-RAY DIFFRACTION3A80 - 113
4X-RAY DIFFRACTION4A114 - 136
5X-RAY DIFFRACTION5A137 - 173
6X-RAY DIFFRACTION6A174 - 349

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