6OB0

Compound 2 bound structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced in HEK293-F cells


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoprotein lipase
A, B, C, D
448Homo sapiensMutation(s): 0 
Gene Names: GPIHBP1HBP1
EC: 3.1.1.34
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P06858 (Homo sapiens)
Explore P06858 
Go to UniProtKB:  P06858
PHAROS:  P06858
GTEx:  ENSG00000175445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06858
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
E, F, G, H
131Homo sapiensMutation(s): 2 
Gene Names: GPIHBP1HBP1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV16 (Homo sapiens)
Explore Q8IV16 
Go to UniProtKB:  Q8IV16
PHAROS:  Q8IV16
GTEx:  ENSG00000277494 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IV16
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M3D (Subject of Investigation/LOI)
Query on M3D

Download Ideal Coordinates CCD File 
AA [auth C]
GA [auth D]
HA [auth D]
K [auth A]
L [auth A]
AA [auth C],
GA [auth D],
HA [auth D],
K [auth A],
L [auth A],
R [auth B],
S [auth B],
Z [auth C]
7-(3-cyano-4-hydroxyphenyl)-N-[2-(morpholin-4-yl)ethyl]dibenzo[b,f]oxepine-10-carboxamide
C28 H25 N3 O4
WKDYAACRENBHRU-UHFFFAOYSA-N
NAG
Query on NAG

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EA [auth D]
FA [auth D]
I [auth A]
J [auth A]
P [auth B]
EA [auth D],
FA [auth D],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
X [auth C],
Y [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
V [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
IA [auth D]
JA [auth D]
M [auth A]
BA [auth C],
CA [auth C],
IA [auth D],
JA [auth D],
M [auth A],
N [auth A],
T [auth B],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
DA [auth C],
KA [auth D],
O [auth A],
W [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.43α = 90
b = 191.42β = 90
c = 97.18γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary