6KEU

Wildtype E53, a microbial HSL esterase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Wildtype E53, a microbial HSL esterase

Yang, X.C.Yingyi, H.Li, Z.Y.Shuling, J.Zhen, R.Zhao, W.Henglin, C.Li, J.X.Xu, X.W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase
A, B, C, D
311Erythrobacter longusMutation(s): 0 
UniProt
Find proteins for A0A074MDU6 (Erythrobacter longus)
Explore A0A074MDU6 
Go to UniProtKB:  A0A074MDU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A074MDU6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D8F (Subject of Investigation/LOI)
Query on D8F

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
S [auth C],
Y [auth D]
(4-nitrophenyl) hexanoate
C12 H15 N O4
OLRXUEYZKCCEKK-UHFFFAOYSA-N
6NA
Query on 6NA

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X [auth C]HEXANOIC ACID
C6 H12 O2
FUZZWVXGSFPDMH-UHFFFAOYSA-N
SO4
Query on SO4

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AA [auth D]
F [auth A]
K [auth B]
L [auth B]
M [auth B]
AA [auth D],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
FA [auth D]
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.605α = 90
b = 129.888β = 90
c = 221.239γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China31770004

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description