1DMT

STRUCTURE OF HUMAN NEUTRAL ENDOPEPTIDASE COMPLEXED WITH PHOSPHORAMIDON

Structural Biology Knowledgebase: 1DMT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 1DMT

Classification: HYDROLASE

Total Structure Weight: 80890.81

Macromolecule Entities
Molecule Chains Length Organism Details
NEUTRAL ENDOPEPTIDASE A 696 Homo sapiens EC#: 3.4.24.11 IUBMB
Fragment: EXTRACELLULAR DOMAIN
Gene Name(s): MME Gene View EPN
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)- L-LEUCYL-L-TRYPTOPHAN
PHOSPHORAMIDON (Synonym)
C23 H34 N3 O10 P
ZPHBZEQOLSRPAK-XLCYBJAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RDF IC50: 0.4 - 200 nM (93 - 100) BindingDB
Ki: 4 nM (94) BindingDB

N/A in BindingMoad
IC50: 2 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000638
Query on PRD_000638
A PHOSPHORAMIDON Glycopeptide /
Enzyme Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.195
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 107.58 α = 90.00
b = 107.58 β = 90.00
c = 112.84 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-12-15
  • Released Date: 2000-12-20
  • Deposition author(s): Oefner, C., D'Arcy, A., Hennig, M., Winkler, F.K., Dale, G.E.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4