7CIP

Microbial Hormone-sensitive lipase E53 wild type


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7W8N


Literature

Microbial Hormone-sensitive lipase E53 wild type

Yang, X.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase
A, B, C, D
314Erythrobacter longusMutation(s): 0 
Gene Names: EH31_02760
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
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D8F (Subject of Investigation/LOI)
Query on D8F

Download Ideal Coordinates CCD File 
MB [auth C],
NC [auth D],
T [auth A],
UA [auth B]
(4-nitrophenyl) hexanoate
C12 H15 N O4
OLRXUEYZKCCEKK-UHFFFAOYSA-N
NPO
Query on NPO

Download Ideal Coordinates CCD File 
LC [auth D],
RA [auth B],
SA [auth B]
P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
6NA
Query on 6NA

Download Ideal Coordinates CCD File 
CC [auth D],
FB [auth C],
G [auth A],
IC [auth D],
U [auth A]
HEXANOIC ACID
C6 H12 O2
FUZZWVXGSFPDMH-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
W [auth A],
X [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AC [auth D]
E [auth A]
EB [auth C]
IB [auth C]
JB [auth C]
AC [auth D],
E [auth A],
EB [auth C],
IB [auth C],
JB [auth C],
LB [auth C],
QA [auth B],
RB [auth D],
XA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO
Query on DIO

Download Ideal Coordinates CCD File 
BA [auth B]1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
BUA
Query on BUA

Download Ideal Coordinates CCD File 
MA [auth B]butanoic acid
C4 H8 O2
FERIUCNNQQJTOY-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
DC [auth D]
IA [auth B]
J [auth A]
JA [auth B]
K [auth A]
DC [auth D],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
NA [auth B],
OA [auth B],
OB [auth C],
PB [auth C],
R [auth A],
S [auth A],
TA [auth B],
ZB [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth C]
BB [auth C]
CA [auth B]
DA [auth B]
AA [auth B],
AB [auth C],
BB [auth C],
CA [auth B],
DA [auth B],
EC [auth D],
F [auth A],
FA [auth B],
H [auth A],
HB [auth C],
I [auth A],
KB [auth C],
MC [auth D],
NB [auth C],
P [auth A],
SB [auth D],
UB [auth D],
VA [auth B],
VB [auth D],
WA [auth C],
WB [auth D],
Y [auth B],
YA [auth C],
Z [auth B],
ZA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CCN
Query on CCN

Download Ideal Coordinates CCD File 
BC [auth D]
CB [auth C]
DB [auth C]
EA [auth B]
FC [auth D]
BC [auth D],
CB [auth C],
DB [auth C],
EA [auth B],
FC [auth D],
GA [auth B],
GB [auth C],
GC [auth D],
HA [auth B],
HC [auth D],
JC [auth D],
KA [auth B],
KC [auth D],
L [auth A],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
PA [auth B],
Q [auth A],
TB [auth D],
V [auth A],
XB [auth D],
YB [auth D]
ACETONITRILE
C2 H3 N
WEVYAHXRMPXWCK-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
QB [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.176 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.576α = 90
b = 129.838β = 90
c = 221.079γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31770004

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description