4FAB

THREE-DIMENSIONAL STRUCTURE OF A FLUORESCEIN-FAB COMPLEX CRYSTALLIZED IN 2-METHYL-2,4-PENTANEDIOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentanediol.

Herron, J.N.He, X.M.Mason, M.L.Voss Jr., E.W.Edmundson, A.B.

(1989) Proteins 5: 271-280

  • DOI: 10.1002/prot.340050404
  • Primary Citation of Related Structures:  
    4FAB

  • PubMed Abstract: 
  • The crystal structure of a fluorescein-Fab (4-4-20) complex was determined at 2.7 A resolution by molecular replacement methods. The starting model was the refined 2.7 A structure of unliganded Fab from an autoantibody (BV04-01) with specificity for single-stranded DNA ...

    The crystal structure of a fluorescein-Fab (4-4-20) complex was determined at 2.7 A resolution by molecular replacement methods. The starting model was the refined 2.7 A structure of unliganded Fab from an autoantibody (BV04-01) with specificity for single-stranded DNA. In the 4-4-20 complex fluorescein fits tightly into a relatively deep slot formed by a network of tryptophan and tyrosine side chains. The planar xanthonyl ring of the hapten is accommodated at the bottom of the slot while the phenylcarboxyl group interfaces with solvent. Tyrosine 37 (light chain) and tryptophan 33 (heavy chain) flank the xanthonyl group and tryptophan 101 (light chain) provides the floor of the combining site. Tyrosine 103 (heavy chain) is situated near the phenyl ring of the hapten and tyrosine 102 (heavy chain) forms part of the boundary of the slot. Histidine 31 and arginine 39 of the light chain are located in positions adjacent to the two enolic groups at opposite ends of the xanthonyl ring, and thus account for neutralization of one of two negative charges in the haptenic dianion. Formation of an enol-arginine ion pair in a region of low dielectric constant may account for an incremental increase in affinity of 2-3 orders of magnitude in the 4-4-20 molecule relative to other members of an idiotypic family of monoclonal antifluorescyl antibodies. The phenyl carboxyl group of fluorescein appears to be hydrogen bonded to the phenolic hydroxyl group of tyrosine 37 of the light chain. A molecule of 2-methyl-2,4-pentanediol (MPD), trapped in the interface of the variable domains just below the fluorescein binding site, may be partly responsible for the decrease in affinity for the hapten in MPD.


    Related Citations: 
    • Differences in Crystal Properties and Ligand Affinities of an Antifluorescyl Fab (4-4-20) in Two Solvent Systems
      Gibson, A.L., Herron, J.N., He, X.-M., Patrick, V.A., Mason, M.L., Lin, J.-N., Kranz, D.M., Vossjunior, E.W., Edmundson, A.B.
      (1988) Proteins 3: 155

    Organizational Affiliation

    Department of Biology, University of Utah, Salt Lake City 84112.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A-KAPPA 4-4-20 FAB (LIGHT CHAIN)A [auth L]219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A-KAPPA 4-4-20 FAB (HEAVY CHAIN)B [auth H]216Mus musculusMutation(s): 0 
Gene Names: Igh-1a
UniProt
Find proteins for P01865 (Mus musculus)
Explore P01865 
Go to UniProtKB:  P01865
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLU (Subject of Investigation/LOI)
Query on FLU

Download Ideal Coordinates CCD File 
C [auth H]2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
C20 H12 O5
YKGGGCXBWXHKIZ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth H](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FDS PDBBind:  4FAB Kd: 8.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Observed: 0.215 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.3α = 82.1
b = 43.9β = 87.3
c = 42.5γ = 84.6
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1990-07-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-09-27
    Changes: Advisory, Atomic model, Non-polymer description, Other, Structure summary