5O5U

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a urea based inhibitor PSMA 1027


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.171 
  • 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 (GCPII) in complex with a urea based inhibitor PSMA 1027

Novakova, Z.Barinka, C.Motlova, L.

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
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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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
9LZ
Query on 9LZ

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A
(2~{S})-2-[[(2~{S})-6-[[(2~{S})-2-[[4-[[[(2~{S})-2-[[(2~{R})-2-[(6-fluoranylpyridin-3-yl)carbonylamino]-3-sulfo-propanoyl]amino]-3-sulfo-propanoyl]amino]methyl]phenyl]carbonylamino]-3-naphthalen-2-yl-propanoyl]amino]-1-oxidanyl-1-oxidanylidene-hexan-2-yl]carbamoylamino]pentanedioic acid
C45 H51 F N8 O18 S2
FRBOTEDIQNCFCM-ISWDJSIVSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.157 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.790α = 90.00
b = 130.412β = 90.00
c = 159.097γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release