9GFG | pdb_00009gfg

BCR Fab from the subset 1 chronic lymphocytic leukaemia case P3129

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-08-09 Released: 2025-08-20 
  • Deposition Author(s): Minici, C., Degano, M.
  • Funding Organization(s): Italian Association for Cancer Research, Worldwide Cancer Research, Italian Ministry of Health

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.246 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Defective cell-autonomous signalling and antigenic polyreactivity of B-cell receptors from chronic lymphocytic leukaemia stereotyped subset 1

Cocomazzi, P.G., Iatrou, A., Minici, C., Degano, M.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BCR P3129 heavy chainA [auth H],
C [auth A],
E [auth C],
G [auth E]		225Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BCR P3129 light chainB [auth L],
D [auth B],
F [auth D],
H [auth F]		215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth G]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
N [auth A],
S [auth C]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
J [auth H]
K [auth H]
L [auth H]
M [auth L]
O [auth A]
J [auth H],
K [auth H],
L [auth H],
M [auth L],
O [auth A],
P [auth A],
Q [auth B],
R [auth B],
T [auth D],
U [auth D],
V [auth D],
W [auth E],
X [auth F],
Y [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.696α = 90
b = 87.891β = 94.59
c = 115.528γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG17032
Italian Association for Cancer ResearchItalyIG25764
Worldwide Cancer ResearchUnited Kingdom19-0096
Italian Ministry of HealthItalyRF-2018-12368231

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release