4PK0

CRYSTAL STRUCTURE OF T4 LYSOZYME-PEPTIDE IN COMPLEX WITH TEICOPLANIN-A2-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report



Literature

X-ray Crystal Structure of Teicoplanin A2-2 Bound to a Catalytic Peptide Sequence via the Carrier Protein Strategy.

Han, S.Le, B.V.Hajare, H.S.Baxter, R.H.Miller, S.J.

(2014) J Org Chem 79: 8550-8556

  • DOI: 10.1021/jo501625f
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We report the X-ray crystal structure of a site-selective peptide catalyst moiety and teicoplanin A2-2 complex. The expressed protein ligation technique was used to couple T4 lysozyme (T4L) and a synthetic peptide catalyst responsible for the selecti ...

    We report the X-ray crystal structure of a site-selective peptide catalyst moiety and teicoplanin A2-2 complex. The expressed protein ligation technique was used to couple T4 lysozyme (T4L) and a synthetic peptide catalyst responsible for the selective phosphorylation of the N-acetylglucosamine sugar in a teicoplanin A2-2 derivative. The T4L-Pmh-dPro-Aib-dAla-dAla construct was crystallized in the presence of teicoplanin A2-2. The resulting 2.3 Å resolution protein-peptide-teicoplanin complex crystal structure revealed that the nucleophilic nitrogen of N-methylimidazole in the Pmh residue is in closer proximity (7.6 Å) to the N-acetylglucosamine than the two other sugar rings present in teicoplanin (9.3 and 20.3 Å, respectively). This molecular arrangement is consistent with the observed selectivity afforded by the peptide-based catalyst when it is applied to a site-selective phosphorylation reaction involving a teicoplanin A2-2 derivative.


    Organizational Affiliation

    Department of Chemistry, Yale University , New Haven, Connecticut 06511, United States.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TEICOPLANIN-A2-2
B
7Actinoplanes teichomyceticusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A
171Escherichia virus T4Mutation(s): 2 
Gene Names: eT4Tp126
EC: 3.2.1.17
Find proteins for D9IEF7 (Enterobacteria phage T4)
Go to UniProtKB:  D9IEF7
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GCS
Query on GCS

Download CCD File 
B
D-GLUCOSAMINE
C6 H13 N O5
MSWZFWKMSRAUBD-QZABAPFNSA-N
 Ligand Interaction
T55
Query on T55

Download CCD File 
A
8-METHYLNONANOIC ACID
C10 H20 O2
OAOABCKPVCUNKO-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002089
Query on PRD_002089
BTEICOPLANIN-A2-2Glycopeptide /  Antibiotic

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Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
3MY
Query on 3MY
B
D-PEPTIDE LINKINGC9 H10 Cl N O3TYR
OMY
Query on OMY
B
L-PEPTIDE LINKINGC9 H10 Cl N O4TYR
AIB
Query on AIB
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
CCS
Query on CCS
A, B
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
MHS
Query on MHS
A, B
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: I 2 2 2
  • Diffraction Data DOI: 10.15785/SBGRID/118 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.923α = 90
b = 63.233β = 90
c = 138.615γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-068649

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 2.0: 2019-12-25
    Changes: Author supporting evidence, Polymer sequence