1PPL

CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PENICILLOPEPSINA [auth E]323Penicillium janthinellumMutation(s): 0 
EC: 3.4.23.20
UniProt
Find proteins for P00798 (Penicillium janthinellum)
Explore P00798 
Go to UniProtKB:  P00798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00798
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1Z7
Query on 1Z7
Download Ideal Coordinates CCD File 
B [auth E]N-(3-methylbutanoyl)-L-valyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl}-L- valinamide
C30 H50 N3 O8 P
ZZHDLOZXEAHENM-KMQNXVAFSA-N
MAN
Query on MAN
Download Ideal Coordinates CCD File 
C [auth E]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
XYS
Query on XYS
Download Ideal Coordinates CCD File 
D [auth E]alpha-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
1Z7 Binding MOAD:  1PPL Ki: 2.8 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_000659 (1Z7)
Query on PRD_000659		B [auth E]IVA-VAL-VAL-LEU(P)-(O)PHE-OMEPeptide-like / Inhibitor
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.5α = 90
b = 46.46β = 115.2
c = 65.93γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2019-07-17
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary