4NGM

Crystal Structure of Glutamate Carboxypeptidase II in a complex with urea-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.170

Literature

Macromolecules
Sequence Display for 4NGM

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 87353.45

Macromolecule Entities
Molecule Chains Length Organism Details
Glutamate carboxypeptidase 2 A 739 Homo sapiens EC#: 3.4.17.21 IUBMB
Fragment: Extracellular domain, UNP residues 44-750
Gene Name(s): FOLH1 Gene View FOLH NAALAD1 PSM PSMA GIG27
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
JB7
Query on JB7

A N-({(1S)-5-[acetyl(4-bromobenzyl)amino]-1- carboxypentyl}carbamoyl)-L-glutamic acid
(S)-2-(3-((S)-5-(N-(4-bromobenzyl)acetamido)- 1-carboxypentyl)ureido)pentanedioic acid (Synonym)
C21 H28 Br N3 O8
ARLQMQGVVFXZCW-IRXDYDNUSA-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)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
JB7 Ki: 0.0449 - 0.045 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.170
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 101.30 α = 90.00
b = 130.19 β = 90.00
c = 158.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-11-02
  • Released Date: 2014-06-18
  • Deposition author(s): Tykvart, J., Pachl, P.

Revision History

  • Version 1_0: 2014-06-18

    Type: Initial release