6KHM

Lipase (Open form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Closed, blocked, and open states of lipase from type II Cutibacterium acnes

Kim, H.J.Lee, B.J.Kwon, A.R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrolase, alpha/beta domain protein
A,
B,
C,
D,
E,
317Cutibacterium acnes HL110PA4Mutation(s): 0 
Gene Names: HMPREF9578_02569
UniProt
Find proteins for E6DAE5 (Cutibacterium acnes HL110PA4)
Explore E6DAE5 
Go to UniProtKB:  E6DAE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6DAE5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DKO (Subject of Investigation/LOI)
Query on DKO

Download Ideal Coordinates CCD File 
BA [auth B],
NA [auth N],
RA [auth R]
octane-1,1-diol
C8 H18 O2
QYPUTBKHHRIDGS-UHFFFAOYSA-N
 Ligand Interaction
DKL (Subject of Investigation/LOI)
Query on DKL

Download Ideal Coordinates CCD File 
AA [auth A],
CA [auth C],
QA [auth Q],
TA [auth T],
WA [auth X]
heptane-1,1-diol
C7 H16 O2
MHIBEGOZTWERHF-UHFFFAOYSA-N
 Ligand Interaction
DKF (Subject of Investigation/LOI)
Query on DKF

Download Ideal Coordinates CCD File 
EA [auth E],
GA [auth G],
IA [auth I],
JA [auth J],
KA [auth K],
EA [auth E],
GA [auth G],
IA [auth I],
JA [auth J],
KA [auth K],
LA [auth L],
MA [auth M],
UA [auth U],
VA [auth V],
XA [auth Y],
YA [auth W]
hexane-1,1-diol
C6 H14 O2
ACCCMOQWYVYDOT-UHFFFAOYSA-N
 Ligand Interaction
DK9 (Subject of Investigation/LOI)
Query on DK9

Download Ideal Coordinates CCD File 
FA [auth F],
OA [auth O],
PA [auth P]
pentane-1,1-diol
C5 H12 O2
UWJJYHHHVWZFEP-UHFFFAOYSA-N
 Ligand Interaction
DK6 (Subject of Investigation/LOI)
Query on DK6

Download Ideal Coordinates CCD File 
DA [auth D],
HA [auth H],
SA [auth S],
ZA [auth Z]
propane-1,1-diol
C3 H8 O2
ULWHHBHJGPPBCO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.857α = 90
b = 185.857β = 90
c = 205.099γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2017R1D1A1B03033857
National Research Foundation (Korea)Korea, Republic Of2018R1A5A2024425

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release