1BZQ

COMPLEX OF A DROMEDARY SINGLE-DOMAIN VHH ANTIBODY FRAGMENT WITH RNASE A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops.

Decanniere, K.Desmyter, A.Lauwereys, M.Ghahroudi, M.A.Muyldermans, S.Wyns, L.

(1999) Structure Fold.Des. 7: 361-370


  • PubMed Abstract: 
  • Camelid serum contains a large fraction of functional heavy-chain antibodies - homodimers of heavy chains without light chains. The variable domains of these heavy-chain antibodies (VHH) have a long complementarity determining region 3 (CDR3) loop th ...

    Camelid serum contains a large fraction of functional heavy-chain antibodies - homodimers of heavy chains without light chains. The variable domains of these heavy-chain antibodies (VHH) have a long complementarity determining region 3 (CDR3) loop that compensates for the absence of the antigen-binding loops of the variable light chains (VL). In the case of the VHH fragment cAb-Lys3, part of the 24 amino acid long CDR3 loop protrudes from the antigen-binding surface and inserts into the active-site cleft of its antigen, rendering cAb-Lys3 a competitive enzyme inhibitor.


    Related Citations: 
    • Crystal Structure of a Camel Single-Domain VH Antibody Fragment in Complex with Lysozyme
      Desmyter, A.,Transue, T.R.,Ghahroudi, M.A.,Thi, M.H.,Poortmans, F.,Hmaers, R.,Muyldermans, S.,WYNS, L.
      (1998) Nat.Struct.Mol.Biol. 9: 803


    Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 St. Genesius-Rode, Belgium. klaas@ultr.vub.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RNASE A)
A, B, C, D
124Bos taurusGene Names: RNASE1 (RNS1)
EC: 3.1.27.5
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ANTIBODY CAB-RN05)
K, L, M, N
124N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 66.520α = 91.43
b = 66.820β = 117.34
c = 69.340γ = 97.33
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance