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- PDB-6yvt: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253 -

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Basic information

Entry
Database: PDB / ID: 6yvt
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253
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


peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / intracellular oxygen homeostasis / labyrinthine layer development / regulation protein catabolic process at postsynapse / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation ...peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / intracellular oxygen homeostasis / labyrinthine layer development / regulation protein catabolic process at postsynapse / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / regulation of modification of postsynaptic structure / cardiac muscle tissue morphogenesis / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / regulation of neuron apoptotic process / negative regulation of DNA-binding transcription factor activity / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to hypoxia / intracellular iron ion homeostasis / response to hypoxia / postsynaptic density / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / 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 signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / q2cbj1_9rhob like domain ...: / 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 signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-PW2 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.847 Å
AuthorsChowdhury, R. / Demetriades, M. / Schofield, C.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Dynamic combinatorial chemistry employing boronic acids/boronate esters leads to potent oxygenase inhibitors.
Authors: Demetriades, M. / Leung, I.K. / Chowdhury, R. / Chan, M.C. / McDonough, M.A. / Yeoh, K.K. / Tian, Y.M. / Claridge, T.D. / Ratcliffe, P.J. / Woon, E.C. / Schofield, C.J.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Egl nine homolog 1
B: Egl nine homolog 1
C: Egl nine homolog 1
D: Egl nine homolog 1
E: Egl nine homolog 1
F: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,21320
Polymers168,5826
Non-polymers2,63214
Water1,02757
1
A: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5043
Polymers28,0971
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5043
Polymers28,0971
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5043
Polymers28,0971
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5043
Polymers28,0971
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6925
Polymers28,0971
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5043
Polymers28,0971
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.456, 103.018, 196.028
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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.: 6
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

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Non-polymers , 5 types, 71 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PW2 / 2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid


Mass: 352.341 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H16N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 6, 2011 / 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: 2.847→50 Å / Num. obs: 40604 / % possible obs: 99.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 48.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.112 / Rrim(I) all: 0.2 / Χ2: 1.098 / Net I/σ(I): 6.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.85-2.9551.8140070.4820.711.07299.6
2.95-3.074.939850.5970.6881.08899.8
3.07-3.214.940340.6930.5131.08199.8
3.21-3.384.940190.8380.3311.06299.50.6670.748
3.38-3.594.940060.920.2051.053990.4140.464
3.59-3.874.940140.9470.1251.06498.90.2520.282
3.87-4.265.340650.980.1021.10999.70.2130.236
4.26-4.875.440700.9910.0561.1299.60.120.133
4.87-6.146.241610.9910.071.1351000.1610.176
6.14-506.142430.9980.0391.15397.70.0880.097

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G19

2g19


Resolution: 2.847→23.753 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 2041 5.04 %
Rwork0.2368 --
obs0.2382 40524 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 57.9 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 211.06 Å2 / Biso mean: 55.0728 Å2 / Biso min: 19.96 Å2
Refinement stepCycle: final / Resolution: 2.847→23.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9117 0 271 57 9445
Biso mean--46.01 37.25 -
Num. residues----1182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0040.0459529
X-RAY DIFFRACTIONf_angle_d0.7956.90912945
X-RAY DIFFRACTIONf_dihedral_angle_d16.442179.965500
X-RAY DIFFRACTIONf_chiral_restr0.0480.1671356
X-RAY DIFFRACTIONf_plane_restr0.0050.0611691
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8474-2.91350.37091550.3157247698
2.9135-2.98620.36191300.30362514100
2.9862-3.06680.36861480.29652521100
3.0668-3.15680.31211430.28362561100
3.1568-3.25850.32251320.26622536100
3.2585-3.37460.30541390.25062528100
3.3746-3.50930.27281120.2527257099
3.5093-3.66850.26281130.2271254898
3.6685-3.86110.24221200.2457254099
3.8611-4.10190.27391430.2376255899
4.1019-4.41670.23761270.20532572100
4.4167-4.85780.2021460.19482567100
4.8578-5.55290.24831400.21052613100
5.5529-6.96660.25251400.24222654100
6.9666-23.7530.231530.21622725100

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