2DN1

1.25A resolution crystal structure of human hemoglobin in the oxy form

Structural Biology Knowledgebase: 2DN1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Observed: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2DN1

Classification: OXYGEN STORAGE / TRANSPORT

Total Structure Weight: 32522.12

Macromolecule Entities
Molecule Chains Length Organism Details
Hemoglobin alpha subunit A 141 Homo sapiens Gene Name(s): HBA1 Gene View HBA2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Hemoglobin beta subunit B 146 Homo sapiens Gene Name(s): HBB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MBN
Query on MBN

A TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXY
Query on OXY

A, B OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Observed: 0.195
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.44 α = 90.00
b = 53.44 β = 90.00
c = 191.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-04-25
  • Released Date: 2006-05-09
  • Deposition author(s): Park, S.-Y., Yokoyama, T., Shibayama, N., Shiro, Y., Tame, J.R.
  • Previous versions: 2DFO

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4