3B75

Crystal Structure of Glycated Human Haemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The effect of hemoglobin glycosylation on diabete linked oxidative stress

Saraswathi, N.T.Syakhovich, V.E.Bokut, S.B.Moras, D.Ruff, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alphaA,
C,
E,
G,
I [auth S]
141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit betaB,
D,
F,
H,
J [auth T]
146Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
GTEx:  ENSG00000244734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
FA [auth S]
IA [auth T]
L [auth A]
BA [auth G],
DA [auth H],
FA [auth S],
IA [auth T],
L [auth A],
O [auth B],
R [auth C],
T [auth D],
W [auth E],
Y [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
GLC
Query on GLC

Download Ideal Coordinates CCD File 
HA [auth T],
N [auth B],
Q [auth C]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
FRU
Query on FRU

Download Ideal Coordinates CCD File 
K [auth A],
V [auth E]
beta-D-fructofuranose
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth G]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
OXY
Query on OXY

Download Ideal Coordinates CCD File 
CA [auth G]
EA [auth H]
GA [auth S]
JA [auth T]
M [auth A]
CA [auth G],
EA [auth H],
GA [auth S],
JA [auth T],
M [auth A],
P [auth B],
S [auth C],
U [auth D],
X [auth E],
Z [auth F]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 237.987α = 90
b = 59.267β = 125.36
c = 137.024γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary