5MHH | pdb_00005mhh

Crystal structure of engineered human lipocalin 2 carrying p-boronophenylalanine at position 36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.233 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Rational Design of an Anticalin-Type Sugar-Binding Protein Using a Genetically Encoded Boronate Side Chain.

Edwardraja, S.Eichinger, A.Theobald, I.Sommer, C.A.Reichert, A.J.Skerra, A.

(2017) ACS Synth Biol 6: 2241-2247

  • DOI: https://doi.org/10.1021/acssynbio.7b00199
  • Primary Citation Related Structures: 
    5MHH

  • PubMed Abstract: 

    The molecular recognition of carbohydrates plays a fundamental role in many biological processes. However, the development of carbohydrate-binding reagents for biomedical research and use poses a challenge due to the generally poor affinity of proteins toward sugars in aqueous solution. Here, we describe the effective molecular recognition of pyranose monosaccharides (in particular, galactose and mannose) by a rationally designed protein receptor based on the human lipocalin scaffold (Anticalin). Complexation relies on reversible covalent cis-diol boronate diester formation with a genetically encoded l-boronophenylalanine (Bpa) residue which was incorporated as a non-natural amino acid at a sterically permissive position in the ligand pocket of the Anticalin, as confirmed by X-ray crystallography. Compared with the metal-ion and/or avidity-dependent oligovalent lectins that prevail in nature, our approach offers a novel and promising route to generate tight sugar-binding reagents both as research reagents and for biomedical applications.


  • Organizational Affiliation
    • Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München , Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany.

Macromolecule Content 

  • Total Structure Weight: 22.16 kDa 
  • Atom Count: 1,557 
  • Modeled Residue Count: 182 
  • Deposited Residue Count: 188 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin188Homo sapiensMutation(s): 5 
Gene Names: LCN2HNLNGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
GTEx:  ENSG00000148346 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.233 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.857α = 90
b = 90.857β = 90
c = 44.2γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationGermanyALTF number 858-2011
Helmholtz-Zentrum BerlinGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 2.0: 2019-04-24
    Changes: Data collection, Polymer sequence
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-10-16
    Changes: Structure summary