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- PDB-5ooh: Human biliverdin IX beta reductase: NADP/Erythrosin extra bluish ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ooh | ||||||
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Title | Human biliverdin IX beta reductase: NADP/Erythrosin extra bluish ternary complex | ||||||
![]() | Flavin reductase (NADPH) | ||||||
![]() | OXIDOREDUCTASE / Biliverdin reductase | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Manso, J.A. / Pereira, P.J.B. | ||||||
![]() | ![]() Title: In silicoand crystallographic studies identify key structural features of biliverdin IX beta reductase inhibitors having nanomolar potency. Authors: Nesbitt, N.M. / Zheng, X. / Li, Z. / Manso, J.A. / Yen, W.Y. / Malone, L.E. / Ripoll-Rozada, J. / Pereira, P.J.B. / Mantle, T.J. / Wang, J. / Bahou, W.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.2 KB | Display | ![]() |
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PDB format | ![]() | 116.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oogC ![]() 1hdoS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
Experimental dataset #2 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() References: UniProt: P30043, flavin reductase (NADPH), biliverdin reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-9ZZ / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→40.3 Å / Num. obs: 65182 / % possible obs: 96.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 3.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.034 / Rrim(I) all: 0.111 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3061 / CC1/2: 0.808 / Rpim(I) all: 0.308 / Rrim(I) all: 0.893 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HDO Resolution: 1.2→32.194 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 12.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→32.194 Å
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Refine LS restraints |
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LS refinement shell |
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