3FCT

MATURE METAL CHELATASE CATALYTIC ANTIBODY WITH HAPTEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural and kinetic evidence for strain in biological catalysis.

Romesberg, F.E.Santarsiero, B.D.Spiller, B.Yin, J.Barnes, D.Schultz, P.G.Stevens, R.C.

(1998) Biochemistry 37: 14404-14409

  • DOI: https://doi.org/10.1021/bi981578c
  • Primary Citation of Related Structures:  
    3FCT

  • PubMed Abstract: 

    A classic hypothesis for enzyme catalysis is the induction of strain in the substrate. This notion was first expressed by Haldane with the lock and key analogy-"the key does not fit the lock perfectly but exercises a certain strain on it" (1). This mechanism has often been invoked to explain the catalytic efficiency of enzymes but has been difficult to establish conclusively (2-7). Here we describe X-ray crystallographic and mutational studies of an antibody metal chelatase which strongly support the notion that this antibody catalyzes metal ion insertion into the porphyrin ring by inducing strain. Analysis of the germline precursor suggests that this strain mechanism arose during the process of affinity maturation in response to a conformationally distorted N-alkylmesoporphyrin.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
A, C
213Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
B, D
216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMP
Query on MMP

Download Ideal Coordinates CCD File 
K [auth B],
P [auth D]
N-METHYLMESOPORPHYRIN
C35 H40 N4 O4
YNWHQWMCLCANDI-YIYRCNGCSA-N
CD
Query on CD

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E [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CA
Query on CA

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F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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H [auth A]
I [auth B]
J [auth B]
L [auth C]
M [auth C]
H [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.29α = 90
b = 100.689β = 90
c = 73.537γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-23
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-01-22
    Changes: Advisory, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description