2H63 | pdb_00002h63

Crystal Structure of Human Biliverdin Reductase A

• PDB DOI: https://doi.org/10.2210/pdb2H63/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-30 Released: 2006-07-04 
• Deposition Author(s): Kavanagh, K., Elkins, J., Ugochukwu, E., Guo, K., Pilka, E., Lukacik, P., Smee, C., Papagrigoriou, E., Bunkoczi, G., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.287 (Depositor), 0.324 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.281 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Biliverdin Reductase A

Kavanagh, K., Elkins, J., Ugochukwu, E., Guo, K., Pilka, E., Lukacik, P., Smee, C., Papagrigoriou, E., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.05 kDa 
• Atom Count: 8,668 
• Modeled Residue Count: 1,131 
• Deposited Residue Count: 1,168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biliverdin reductase A	A, B, C, D	292	Homo sapiens	Mutation(s): 0  Gene Names: BLVRA EC: 1.3.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53004 (Homo sapiens) Explore P53004  Go to UniProtKB:  P53004
PHAROS:  P53004 GTEx:  ENSG00000106605

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], F [auth B], G [auth C], H [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.287 (Depositor), 0.324 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.281 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.787	α = 90
b = 92.747	β = 90
c = 147.755	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Kavanagh, K., Elkins, J., Ugochukwu, E., Guo, K., Pilka, E., Lukacik, P., Smee, C., Papagrigoriou, E., Bunkoczi, G., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description