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- PDB-8j1k: co-crystal structure of non-carboxylic acid inhibitor with PHD2 -

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Basic information

Entry
Database: PDB / ID: 8j1k
Titleco-crystal structure of non-carboxylic acid inhibitor with PHD2
ComponentsEgl nine homolog 1
KeywordsOXIDOREDUCTASE/INHIBITOR / OXIDOREDUCTASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis ...hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / regulation of modification of postsynaptic structure / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of DNA-binding transcription factor activity / cellular response to hypoxia / intracellular iron ion homeostasis / postsynaptic density / response to hypoxia / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm / cytosol
Similarity search - Function
Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / : / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 Å
AuthorsXu, J. / Fu, Y. / Ding, X. / Meng, Q. / Wang, L. / Zhang, M. / Ding, X. / Ren, F. / Zhavoronkov, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: co-crystal structure of non-carboxylic acid inhibitor with PHD2
Authors: Xu, J. / Fu, Y. / Ding, X. / Meng, Q. / Wang, L. / Man, Z. / Ding, X. / Ren, F. / Zhavoronkov, A.
History
DepositionApr 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9443
Polymers24,4991
Non-polymers4452
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-6 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.843, 80.843, 63.899
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

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Components

#1: Protein Egl nine homolog 1 / Hypoxia-inducible factor prolyl hydroxylase 2 / HIF-PH2 / HIF-prolyl hydroxylase 2 / HPH-2 / Prolyl ...Hypoxia-inducible factor prolyl hydroxylase 2 / HIF-PH2 / HIF-prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 24498.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Chemical ChemComp-SY6 / N-[(6-cyanopyridin-3-yl)methyl]-5-oxidanyl-2-[(3R)-3-oxidanylpyrrolidin-1-yl]-1,7-naphthyridine-6-carboxamide


Mass: 390.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18N6O3 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4 phosphate monobasic,0.1M Tris,8.5,50% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18057 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18057 Å / Relative weight: 1
ReflectionResolution: 2.45→47.2 Å / Num. obs: 8837 / % possible obs: 100 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.6
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 1.05 / Num. unique obs: 966

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.451→47.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.534 / SU ML: 0.255 / Cross valid method: FREE R-VALUE / ESU R: 0.572 / ESU R Free: 0.34
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3084 488 5.53 %
Rwork0.242 8336 -
all0.246 --
obs-8824 99.977 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 76.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.638 Å20.319 Å20 Å2
2--0.638 Å2-0 Å2
3----2.069 Å2
Refinement stepCycle: LAST / Resolution: 2.451→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 30 30 1629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121645
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161475
X-RAY DIFFRACTIONr_angle_refined_deg0.7561.6552215
X-RAY DIFFRACTIONr_angle_other_deg0.2681.5743434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.1555.38513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99810270
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.3421076
X-RAY DIFFRACTIONr_chiral_restr0.0350.2228
X-RAY DIFFRACTIONr_chiral_restr_other0.020.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02347
X-RAY DIFFRACTIONr_nbd_refined0.2130.2286
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.21403
X-RAY DIFFRACTIONr_nbtor_refined0.180.2807
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.243
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.24
X-RAY DIFFRACTIONr_nbd_other0.1680.217
X-RAY DIFFRACTIONr_mcbond_it2.6627.859790
X-RAY DIFFRACTIONr_mcbond_other2.6637.854789
X-RAY DIFFRACTIONr_mcangle_it4.04111.768984
X-RAY DIFFRACTIONr_mcangle_other4.03911.773985
X-RAY DIFFRACTIONr_scbond_it2.4137.923855
X-RAY DIFFRACTIONr_scbond_other2.4017.928853
X-RAY DIFFRACTIONr_scangle_it3.72411.8111231
X-RAY DIFFRACTIONr_scangle_other3.72311.8091232
X-RAY DIFFRACTIONr_lrange_it5.99390.931835
X-RAY DIFFRACTIONr_lrange_other5.97690.8911832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.451-2.5140.267390.18614X-RAY DIFFRACTION100
2.514-2.5830.325260.291574X-RAY DIFFRACTION100
2.583-2.6570.401340.286601X-RAY DIFFRACTION100
2.657-2.7390.367390.299545X-RAY DIFFRACTION100
2.739-2.8280.335270.302551X-RAY DIFFRACTION100
2.828-2.9270.47420.335520X-RAY DIFFRACTION100
2.927-3.0370.385260.312516X-RAY DIFFRACTION100
3.037-3.1610.375310.294484X-RAY DIFFRACTION100
3.161-3.3010.388330.298463X-RAY DIFFRACTION99.7988
3.301-3.4610.345180.263464X-RAY DIFFRACTION100
3.461-3.6470.345270.282423X-RAY DIFFRACTION100
3.647-3.8670.291220.259421X-RAY DIFFRACTION100
3.867-4.1320.323180.258390X-RAY DIFFRACTION100
4.132-4.460.326320.221349X-RAY DIFFRACTION100
4.46-4.8820.236260.198325X-RAY DIFFRACTION100
4.882-5.450.22130.211301X-RAY DIFFRACTION100
5.45-6.280.256130.231266X-RAY DIFFRACTION100
6.28-7.6570.34890.227235X-RAY DIFFRACTION100
7.657-10.690.249110.171181X-RAY DIFFRACTION100
10.69-47.20.27420.208113X-RAY DIFFRACTION100

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