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- PDB-6yvx: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic BB-287 -

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Basic information

Entry
Database: PDB / ID: 6yvx
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic BB-287
ComponentsEgl nine homolog 1
KeywordsOXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION 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 / 2-oxoglutarate-dependent dioxygenase activity ...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 / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis / 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 / cytosol / cytoplasm
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
4-(isoquinolin-3-ylamino)-4-oxobutanoic acid / BICARBONATE ION / : / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChowdhury, R. / Banerji, B. / Schofield, C.J.
Citation
Journal: Sci Rep / Year: 2020
Title: Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2.
Authors: Chowdhury, R. / Abboud, M.I. / McAllister, T.E. / Banerji, B. / Bhushan, B. / Sorensen, J.L. / Kawamura, A. / Schofield, C.J.
#1: Journal: ACS Chem. Biol. / Year: 2013
Title: Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases.
Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / ...Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / Kawamura, A. / Lee, M.K. / van Eeden, F. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,4574
Polymers28,0971
Non-polymers3603
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-7 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.947, 109.947, 39.221
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 28096.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (RESIDUES 181-426) / Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-2JP / 4-(isoquinolin-3-ylamino)-4-oxobutanoic acid


Mass: 244.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.71 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sample: (20 mg/ml PHD2 + 1 mM FeSO4 + 2 mM compound); Reservoir: 1.6-2.0 M (NH4)2SO4, 2-8% dioxane, 0.1 M MES-Na pH 6.5, and 1 mM FeSO4; hanging drop vapour diffusion

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→95.217 Å / Num. obs: 25415 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 31.2 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.027 / Rrim(I) all: 0.093 / Rsym value: 0.088 / Net I/av σ(I): 4.6 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.911.41.3192.436600.4061.381.319100
1.9-2.0111.50.693134870.2110.7250.693100
2.01-2.1510.80.364232800.1150.3820.364100
2.15-2.3211.40.2163.330570.0670.2260.216100
2.32-2.5511.70.1454.828080.0440.1510.145100
2.55-2.8510.90.1046.225640.0330.110.104100
2.85-3.2911.90.0797.822700.0240.0830.079100
3.29-4.0211.10.0649.419200.020.0670.064100
4.02-5.6911.50.05410.915050.0160.0560.054100
5.69-47.60810.50.0667.28640.0210.0690.06699.8

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G19

2g19


Resolution: 1.8→47.608 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1892 1342 5.29 %
Rwork0.1595 --
obs0.161 25353 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 59.1 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 163.12 Å2 / Biso mean: 48.838 Å2 / Biso min: 19.55 Å2
Refinement stepCycle: final / Resolution: 1.8→47.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 35 128 1879
Biso mean--46.4 53.11 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0140.1451844
X-RAY DIFFRACTIONf_angle_d1.2028.5842505
X-RAY DIFFRACTIONf_dihedral_angle_d16.645178.0081086
X-RAY DIFFRACTIONf_chiral_restr0.0830.546266
X-RAY DIFFRACTIONf_plane_restr0.0090.044331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.86430.26821210.2431235199
1.8643-1.9390.2331430.20812361100
1.939-2.02720.20141380.17682367100
2.0272-2.13410.20521460.16582367100
2.1341-2.26780.16661260.14582407100
2.2678-2.44290.18861220.14832432100
2.4429-2.68870.20931280.16422391100
2.6887-3.07780.16731370.1582418100
3.0778-3.87740.17381350.14542425100
3.8774-47.6080.19291460.15952492100
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)
10.8972-0.3751-0.05331.21040.23330.1886-0.1755-0.1034-0.66290.42550.0730.37880.9273-0.2522-0.07120.5368-0.02460.00850.30280.11150.439634.76825.35463.2985
24.64763.0931-0.23522.1640.42362.2497-0.0092-0.63760.24530.4328-0.07660.59930.0922-0.79750.13660.4239-0.00890.1020.59930.03610.324425.078123.938214.4367
35.77960.3368-0.35976.2966-0.57184.4623-0.55080.14620.695-0.3619-0.2036-0.1328-1.16460.55770.16920.6263-0.038-0.04920.36530.03120.595433.013238.76352.0196
44.41890.50670.02643.7306-0.26346.0562-0.2579-0.17210.67010.24640.05770.2906-0.8701-0.04010.23760.4397-0.0163-0.07490.3320.00130.4134.716633.17377.8841
53.736-0.65280.73352.95210.43682.755-0.0669-0.1209-0.06110.31590.0347-0.28880.12890.09130.01910.2566-0.0151-0.03920.240.07530.280240.274818.44335.2089
63.5944-0.33750.64074.40651.12063.95920.12620.4319-0.457-0.3637-0.12610.45770.2162-0.4691-0.01570.2444-0.0135-0.06220.32730.06430.31628.086418.5885-6.8829
73.8959-1.1223-0.1543.8030.69062.31190.06050.1659-0.0264-0.2339-0.09830.08420.2183-0.2530.03120.2098-0.0354-0.03030.25340.06830.19933.090818.4699-3.5568
82.5736-1.57541.9352.3056-0.17432.33660.0382-0.1827-0.3470.09910.1292-0.26460.13830.3216-0.11170.21020.009-0.05770.23780.03520.303545.20919.89164.3387
90.88712.65260.89338.42892.1062.248-0.07680.01131.00950.34860.4960.8713-0.8861-0.0690.78220.4003-0.06080.1060.5575-0.00030.533963.676629.91387.8721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 182 through 215 )A182 - 215
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 231 )A216 - 231
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 246 )A232 - 246
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 266 )A247 - 266
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 329 )A267 - 329
6X-RAY DIFFRACTION6chain 'A' and (resid 330 through 353 )A330 - 353
7X-RAY DIFFRACTION7chain 'A' and (resid 354 through 382 )A354 - 382
8X-RAY DIFFRACTION8chain 'A' and (resid 383 through 398 )A383 - 398
9X-RAY DIFFRACTION9chain 'A' and (resid 399 through 414 )A399 - 414

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