7ZB0

macrocyclase OphP with 15mer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for the enzymatic macrocyclization of multiply backbone N-methylated peptides

Matabaro, E.Song, H.Gherlone, F.Sonderegger, L.Giltrap, A.Liver, S.Gossert, A.Kunzler, M.Naismith, J.H.

(2022) bioRxiv 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prolyl endopeptidase
A, B, C, D
745Omphalotus oleariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
15mer
E, F, G, H
15Omphalotus oleariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
M [auth C],
Q [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth B]
K [auth C]
L [auth C]
R [auth D]
S [auth D]
I [auth B],
K [auth C],
L [auth C],
R [auth D],
S [auth D],
T [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
J [auth B]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
N [auth C]
O [auth C]
P [auth C]
U [auth D]
V [auth D]
N [auth C],
O [auth C],
P [auth C],
U [auth D],
V [auth D],
W [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
IML
Query on IML
E, F, G, H
L-PEPTIDE LINKINGC7 H15 N O2ILE
MVA
Query on MVA
E, F, G, H
L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
E, F, G, H
PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.22α = 113.04
b = 106.18β = 101.67
c = 114.79γ = 93.24
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R018189/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Derived calculations, Refinement description