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- PDB-4ai8: FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH DAMINOZIDE -

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Basic information

Entry
Database: PDB / ID: 4ai8
TitleFACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH DAMINOZIDE
ComponentsHYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
KeywordsOXIDOREDUCTASE / DIOXYGENASE / METAL-BINDING / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / TRANSCRIPTION AND EPIGENETIC REGULATION / ANKYRIN REPEAT DOMAIN / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR
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 / carboxylic acid binding / positive regulation of vasculogenesis / 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 / 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 / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / 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. / JmjC domain / JmjC domain profile. / Jelly Rolls / RmlC-like jelly roll fold / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DAMINOZIDE / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKing, O.N.F. / Chowdhury, R. / Rose, N.R. / McDonough, M.A. / Clifton, I.J. / Schofield, C.J. / Kawamura, A.
CitationJournal: J. Med. Chem. / Year: 2012
Title: Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases.
Authors: Rose, N.R. / Woon, E.C. / Tumber, A. / Walport, L.J. / Chowdhury, R. / Li, X.S. / King, O.N. / Lejeune, C. / Ng, S.S. / Krojer, T. / Chan, M.C. / Rydzik, A.M. / Hopkinson, R.J. / Che, K.H. / ...Authors: Rose, N.R. / Woon, E.C. / Tumber, A. / Walport, L.J. / Chowdhury, R. / Li, X.S. / King, O.N. / Lejeune, C. / Ng, S.S. / Krojer, T. / Chan, M.C. / Rydzik, A.M. / Hopkinson, R.J. / Che, K.H. / Daniel, M. / Strain-Damerell, C. / Gileadi, C. / Kochan, G. / Leung, I.K. / Dunford, J. / Yeoh, K.K. / Ratcliffe, P.J. / Burgess-Brown, N. / von Delft, F. / Muller, S. / Marsden, B. / Brennan, P.E. / McDonough, M.A. / Oppermann, U. / Klose, R.J. / Schofield, C.J. / Kawamura, A.
History
DepositionFeb 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
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 / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 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)41,59311
Polymers40,6111
Non-polymers98210
Water2,432135
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)83,18522
Polymers81,2212
Non-polymers1,96420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6740 Å2
ΔGint-246.3 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.757, 86.757, 145.481
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-2024-

HOH

21A-2025-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 40610.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase

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Non-polymers , 5 types, 145 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DZA / DAMINOZIDE


Mass: 160.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.1 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES PH7.5, 1.6 M AMMONIUM SULFATE, 6% PEG400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 22, 2010 / Details: VARIMAX HF
RadiationMonochromator: CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→28.37 Å / Num. obs: 21975 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2K

1h2k


Resolution: 2.4→28.37 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 522161.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1180 5.3 %RANDOM
Rwork0.231 ---
obs0.231 21975 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.717 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 60.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20 Å2
2---3.83 Å20 Å2
3---7.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 55 135 2897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.892.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 107 4.9 %
Rwork0.339 2192 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DZA.PARDZA.TOP
X-RAY DIFFRACTION5GOL.PARGOL.TOP

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