4ODC

Crystal structure of Trematomus bernacchii hemoglobin in a partially cyanided state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural modifications induced by the switch from an endogenous bis-histidyl to an exogenous cyanomet hexa-coordination in a tetrameric haemoglobin

Mazzarella, L.Merlino, A.Vitagliano, L.Verde, C.di Prisco, G.Peisach, J.Vergara, A.

(2014) RSC Adv 4: 25852-25856


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alphaA143Trematomus bernacchiiMutation(s): 1 
Gene Names: hba
Find proteins for P80043 (Pseudotrematomus bernacchii)
Explore P80043 
Go to UniProtKB:  P80043
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit betaB146Trematomus bernacchiiMutation(s): 0 
Gene Names: hbb
Find proteins for P80044 (Pseudotrematomus bernacchii)
Explore P80044 
Go to UniProtKB:  P80044
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CYN
Query on CYN

Download CCD File 
A, B
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.88α = 90
b = 87.88β = 99.66
c = 55.25γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHELXSphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Advisory, Database references, Derived calculations