6C5K

S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Subtle changes in the combining site of the Chlamydiaceae-specific mAb S25-23 increase antibody-carbohydrate binding affinity by an order of magnitude.

Haji-Ghassemi, O.Muller-Loennies, S.Brooks, C.L.MacKenzie, C.R.Caveney, N.Van Petegem, F.Brade, L.Kosma, P.Brade, H.Evans, S.V.

(2018) Biochemistry --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IgG1 Fab Heavy Chain
H, A
218Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q99LC4 (Mus musculus)
Go to UniProtKB:  Q99LC4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IgG1 Fab Light Chain (Kappa)
L, B
219Mus musculusMutation(s): 0 
Gene Names: LC
Find proteins for A0A0F7R5U8 (Mus musculus)
Go to UniProtKB:  A0A0F7R5U8
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, H
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Z9M
Query on Z9M

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Download CCD File 
A, H
2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose
C6 H14 N O8 P
QWDBGVNDGYUIAC-QZABAPFNSA-N
 Ligand Interaction
KDO
Query on KDO

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Download CCD File 
A, H
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
NO3
Query on NO3

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Download CCD File 
B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
GP1
Query on GP1

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Download CCD File 
A, H
GLUCOSAMINE 1-PHOSPHATE
C6 H14 N O8 P
YMJBYRVFGYXULK-QZABAPFNSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, H
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 171.649α = 90.00
b = 62.710β = 116.09
c = 107.071γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)CanadaDiscovery Grant 171356-2013

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release