4B4Z

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of a Complex between Actinomadura R39 Dd-Peptidase and a Boronate Inhibitor

Sauvage, E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
A, B, C, D
466Actinomadura sp. R39Mutation(s): 0 
EC: 3.4.16.4
UniProt
Find proteins for P39045 (Actinomadura sp. (strain R39))
Explore P39045 
Go to UniProtKB:  P39045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39045
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BSF
Query on BSF

Download Ideal Coordinates CCD File 
E [auth A],
EA [auth D],
O [auth B],
W [auth C]
{[(benzylsulfonyl)amino]methyl}boronic acid
C8 H12 B N O4 S
TTWWUAQISBIHPB-UHFFFAOYSA-N
SO4
Query on SO4

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AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
H [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
N [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

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F [auth A],
FA [auth D],
G [auth A],
GA [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.123α = 90
b = 90.692β = 94.52
c = 105.729γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary