Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18197.48 
• Atom Count: 1296 
• Residue Count: 153 
• Unique protein chains: 1

1BVC

STRUCTURE OF A BILIVERDIN APOMYOGLOBIN COMPLEX (FORM D) AT 118 K

• DOI: 10.2210/pdb1BVC/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter catodon


• Deposited: 1994-12-16 Released: 1995-07-31 
• Deposition Author(s): Wagner, U.G., Mueller, N., Schmitzberger, W., Falk, H., Kratky, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Work: 0.194 

Literature

Structure determination of the biliverdin apomyoglobin complex: crystal structure analysis of two crystal forms at 1.4 and 1.5 A resolution.

Wagner, U.G., Muller, N., Schmitzberger, W., Falk, H., Kratky, C.

(1995) J.Mol.Biol. 247: 326-337

• PubMed: 7707378 
• Primary Citation of Related Structures:  
  1BVD


• PubMed Abstract: 
  

Crystal structure determinations of two orthorhombic (P2(1)2(1)2(1)) crystal modifications of the biliverdin apomyoglobin complex are described. The two structures were determined by X-ray diffraction at 100 K to a resolution of 1.5 A and 1.4 A. Both crystal forms were grown by hanging-drop techniques, using phosphate as precipitant. The structures were solved by molecular replacement and refined to final R-values of 19.4% and 21.2%. Both structures are very similar with respect to the binding site and the conformation of the biliverdin chromophore, which occurs in a (P) helical conformation. It is located within the heme pocket, very close in position and orientation to the heme binding site in myoglobin. Two water molecules not present in the crystal structure of myoglobin are sequestered within the heme pocket in the biliverdin-apomyoglobin complex, and they are engaged in hydrogen bonding to the biliverdin and to the protein. Comparison with structural results from an earlier NMR study of the same complex shows good agreement.

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Related Citations: 

• Nuclear-Magnetic-Resonance Investigations of the Biliverdin Apomyoglobin Complex
  Marko, H.,Mueller, N.,Falk, H.
  (1990) Eur.J.Biochem. 193: 573




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Organizational Affiliation: 

Institut für Physikalische Chemie, Karl-Franzens-Universität, Graz, Austria.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
APOMYOGLOBIN	A	153	Physeter catodon	Mutation(s): 0  Gene Names: MB
Find proteins for P02185 (Physeter catodon) Go to Gene View: MB Go to UniProtKB:  P02185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
BLA	A	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 33.653	α = 90.00
b = 58.863	β = 90.00
c = 76.379	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	model building
XDS	data reduction
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-12-16 
• Released Date: 1995-07-31 
• Deposition Author(s): Wagner, U.G., Mueller, N., Schmitzberger, W., Falk, H., Kratky, C.

Revision History 

• Version 1.0: 1995-07-31
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance