4OME

X-ray structure of human glutamate carboxypeptidase II in complex with DCCBL, a urea based inhibitor with distal carborane moiety


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray structure of human glutamate carboxypeptidase II in complex with DCCBL, a urea based inhibitor with distal carborane moiety

Barinka, C.Ptacek, J.Novakova, Z.Byun, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate carboxypeptidase 2
A
707Homo sapiensMutation(s): 0 
Gene Names: FOLH1 (FOLH, NAALAD1, PSM, PSMA)
EC: 3.4.17.21
Find proteins for Q04609 (Homo sapiens)
Go to Gene View: FOLH1
Go to UniProtKB:  Q04609
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
DGQ
Query on DGQ

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A
(S)-2-(3-((S)-1-carboxy-5-(1,2-dicarba-closo-dodecarboranylamido) pentyl)ureido)pentanedioic acid
DCCBL
C15 H31 B10 N3 O8
NYWNLUFFIRQESZ-YUMQZZPRSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.157 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.316α = 90.00
b = 130.564β = 90.00
c = 158.073γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
XDSdata scaling
REFMACrefinement
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release