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- PDB-1he3: Human biliverdin IX beta reductase: NADP/mesobiliverdin IV alpha ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1he3 | |||||||||
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Title | Human biliverdin IX beta reductase: NADP/mesobiliverdin IV alpha ternary complex | |||||||||
![]() | BILIVERDIN IX BETA REDUCTASE | |||||||||
![]() | BILIVERDIN-IX BETA REDUCTASE / FOETAL METABOLISM / HAEM DEGRADATION / FLAVIN REDUCTASE / DIAPHORASE / GREEN HAEM BINDING PROTEIN / METHAEMOGLOBIN REDUCTASE / ALPHA/BETA DINUCLEOTIDE BINDING FOLD | |||||||||
Function / homology | ![]() biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process ...biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / flavin reductase (NADPH) / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pereira, P.J.B. / Macedo-Ribeiro, S. / Parraga, A. / Perez-Luque, R. / Cunningham, O. / Darcy, K. / Mantle, T.J. / Coll, M. | |||||||||
![]() | ![]() Title: Structure of Human Biliverdin Ix Beta Reductase, an Early Fetal Bilirubin Ix Producing Enzyme Authors: Pereira, P.J.B. / Macedo-Ribeiro, S. / Parraga, A. / Perez-Luque, R. / Cunningham, O. / Darcy, K. / Mantle, T.J. / Coll, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.5 KB | Display | ![]() |
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PDB format | ![]() | 44.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 547.3 KB | Display | ![]() |
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Full document | ![]() | 556.1 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hdoSC ![]() 1he2C ![]() 1he4C ![]() 1he5C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | BIOLOGICAL_UNIT: MONOMER |
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Components
#1: Protein | Mass: 22148.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-MBV / |
#4: Water | ChemComp-HOH / |
Sequence details | THE PDB ENTRY CONTAINS AN EXTRA N-TERMINAL METHIONINE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 40.4 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 30% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5. NADP ADDED TO A FINAL CONCENTRATION OF 2.5 MM | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: May 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.7 Å / Num. obs: 42097 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Rmerge(I) obs: 0.183 / % possible all: 98.6 |
Reflection | *PLUS Num. measured all: 161312 / Rmerge(I) obs: 0.08 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HDO Resolution: 1.4→20 Å / Num. parameters: 17592 / Num. restraintsaints: 21427 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 13 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1860.38 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97/2 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rwork: 0.132 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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