1LMK | pdb_00001lmk

THE STRUCTURE OF A BIVALENT DIABODY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work: 
    0.200 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1LMK

This is version 1.4 of the entry. See complete history

Literature

Crystal structure of a diabody, a bivalent antibody fragment.

Perisic, O.Webb, P.A.Holliger, P.Winter, G.Williams, R.L.

(1994) Structure 2: 1217-1226

  • DOI: https://doi.org/10.1016/s0969-2126(94)00123-5
  • Primary Citation Related Structures: 
    1LMK

  • PubMed Abstract: 

    Diabodies are dimeric antibody fragments. In each polypeptide, a heavy-chain variable domain (VH) is linked to a light-chain variable domain (VL) but unlike single-chain Fv fragments, each antigen-binding site is formed by pairing of one VH and one VL domain from the two different polypeptides. Diabodies thus have two antigen-binding sites, and can be bispecific. Direct structural evidence is lacking for the connections and dimeric interactions between the two polypeptides of the diabody. The 2.6 A resolution structure has been determined for a bivalent diabody with a flexible five-residue polypeptide linker between the (amino-terminal) VH and (carboxy-terminal) VL domains. The asymmetric unit of the crystal consists of four polypeptides comprising two diabodies; for one of these polypeptides the linker can be traced between the VH and VL domains. Within each diabody the two associated VH and VL domains make back-to-back interactions through the VH domains, and there is an extensive VL-VL interface between the two diabodies in the asymmetric unit. The structure of the diabody is very similar to that which had been predicted by molecular modelling. Diabodies directed against cell-surface antigens should be capable of bringing together two cells, such as in cell-targeted therapy, because the two antigen-binding sites of the diabody are at opposite ends of the molecule and separated by approximately 65 A.


  • Organizational Affiliation
    • Centre for Protein Engineering, MRC Centre, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 104.31 kDa 
  • Atom Count: 7,613 
  • Modeled Residue Count: 952 
  • Deposited Residue Count: 952 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODYA,
B [auth C],
C [auth E],
D [auth G]
238Mus musculusMutation(s): 0 
Gene Names: L5MK16

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work:  0.200 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.14α = 90
b = 80.71β = 99.81
c = 88.01γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-03-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-10-30
    Changes: Structure summary