6C5H

S25-5 Fab in complex with Chlamydiaceae-specific LPS antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 

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
Fab Heavy Chain (IgG1)
H
218Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q99LC4 (Mus musculus)
Go to UniProtKB:  Q99LC4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab Light Chain (IgG1 Kappa)
L
219Mus musculusMutation(s): 0 
Gene Names: LC
Find proteins for A0A0F7R5U8 (Mus musculus)
Go to UniProtKB:  A0A0F7R5U8
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
L
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
H
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
H
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Z9M
Query on Z9M

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

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H
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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H
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
KDO
Query on KDO

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Download CCD File 
H
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
GP1
Query on GP1

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.146α = 90.00
b = 128.957β = 90.00
c = 135.428γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing
HKL-2000data reduction

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