4QN9

Structure of human NAPE-PLD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.214

Literature

Macromolecules
Sequence Display for 4QN9

Classification: HYDROLASE

Total Structure Weight: 97673.04

Macromolecule Entities
Molecule Chains Length Organism Details
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D A, B 393 Homo sapiens EC#: 3.1.4.54 IUBMB
Gene Name(s): NAPEPLD Gene View C7orf18
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Hydrolases

Protein Name: N-acylphosphatidylethanolamine-hydrolyzing phospholipase D


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3PE
Query on 3PE

A, B 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
3-SN-PHOSPHATIDYLETHANOLAMINE (Synonym)
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DXC
Query on DXC

A, B (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN- 24-OIC ACID
DEOXYCHOLIC ACID (Synonym)
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.214
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 95.10 α = 90.00
b = 95.10 β = 90.00
c = 444.17 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-06-17
  • Released Date: 2015-06-17
  • Deposition author(s): Garau, G.

Revision History

  • Version 1_0: 2015-06-17

    Type: Initial release

  • Version 1_1: 2017-11-22

    Type: Refinement description