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- PDB-8k4k: Crystal structure of human Biliverdin IX-beta reductase B with Ol... -

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Basic information

Entry
Database: PDB / ID: 8k4k
TitleCrystal structure of human Biliverdin IX-beta reductase B with Olsalazine carbon derivative
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE/INHIBITOR / platelets / NADP / OXIDOREDUCTASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation ...FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / peptidyl-cysteine S-nitrosylase activity / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHa, J.H. / Jung, H.M. / dela Cerna, M.V.C. / Burlison, J.A. / Lee, D. / Ryu, K.S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Other governmentC320000 Korea, Republic Of
National Research Foundation (NRF, Korea)2023R1A2C1006973 Korea, Republic Of
National Research Foundation (NRF, Korea)2022H1D3A2A02093655 Korea, Republic Of
CitationJournal: Pharmaceutics / Year: 2024
Title: An Innovative Inhibitor with a New Chemical Moiety Aimed at Biliverdin IX beta Reductase for Thrombocytopenia and Resilient against Cellular Degradation.
Authors: Jung, H.M. / Ha, J.H. / Dela Cerna, M.V.C. / Burlison, J.A. / Choi, J. / Kim, B.R. / Bang, J.K. / Ryu, K.S. / Lee, D.
History
DepositionJul 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin reductase (NADPH)
B: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,84811
Polymers44,2972
Non-polymers2,5529
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-23 kcal/mol
Surface area17230 Å2
Unit cell
Length a, b, c (Å)82.143, 117.304, 41.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-560-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Flavin reductase (NADPH) / FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / ...FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / GHBP / NADPH-dependent diaphorase / NADPH-flavin reductase / FLR


Mass: 22148.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRB, FLR / Production host: Escherichia coli (E. coli)
References: UniProt: P30043, flavin reductase (NADPH), biliverdin reductase

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Non-polymers , 5 types, 359 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-VE2 / 5-[(E)-2-(3-carboxy-4-oxidanyl-phenyl)ethenyl]-2-oxidanyl-benzoic acid


Mass: 300.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.9~2.0M Ammonium sulfate, 0.1M Bis-tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.7→33.91 Å / Num. obs: 44971 / % possible obs: 99.86 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05728 / Rpim(I) all: 0.01784 / Rrim(I) all: 0.06011 / Net I/σ(I): 23.03
Reflection shellResolution: 1.7→1.762 Å / Rmerge(I) obs: 0.2544 / Mean I/σ(I) obs: 3.83 / CC1/2: 0.936 / Rpim(I) all: 0.1023 / Rrim(I) all: 0.2755

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.91 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 2253 5.01 %
Rwork0.1612 --
obs0.1627 44963 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→33.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 169 350 3613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083342
X-RAY DIFFRACTIONf_angle_d1.0574574
X-RAY DIFFRACTIONf_dihedral_angle_d15.657476
X-RAY DIFFRACTIONf_chiral_restr0.058532
X-RAY DIFFRACTIONf_plane_restr0.008576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.25061500.18792596X-RAY DIFFRACTION99
1.74-1.780.24261330.17182615X-RAY DIFFRACTION100
1.78-1.820.20871410.1712637X-RAY DIFFRACTION100
1.82-1.870.20931350.17592609X-RAY DIFFRACTION100
1.87-1.930.22291360.17542655X-RAY DIFFRACTION100
1.93-1.990.22971400.16972654X-RAY DIFFRACTION100
1.99-2.060.19221320.16012636X-RAY DIFFRACTION100
2.06-2.140.1841400.15182643X-RAY DIFFRACTION100
2.14-2.240.17141350.16222661X-RAY DIFFRACTION100
2.24-2.360.1931360.16372664X-RAY DIFFRACTION100
2.36-2.510.22281600.1662628X-RAY DIFFRACTION100
2.51-2.70.21951460.16532680X-RAY DIFFRACTION100
2.7-2.970.18061340.1722715X-RAY DIFFRACTION100
2.97-3.40.1851430.15942693X-RAY DIFFRACTION100
3.4-4.280.17071440.14412733X-RAY DIFFRACTION100
4.28-33.910.17111480.15752891X-RAY DIFFRACTION100

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