4JYW | pdb_00004jyw

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with CTT1057

PDB DOI: https://doi.org/10.2210/pdb4JYW/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2013-04-01 Released: 2014-04-02
Deposition Author(s): Barinka, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.181 (Depositor), 0.192 (DCC)
R-Value Work:
0.158 (Depositor), 0.172 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

A high affinity 18F-labeled phosphoramidate peptidomimetic inhibitor as a PSMA-targeted PET imaging agent for prostate cancer

Ganguly, T., Dannoon, S., Geruntho, J.G., Hopkins, M.R., Murphy, S., Cahaya, H., Blecha, J.E., Jivan, S., Barinka, C., Jones, E.F., VanBrocklin, H.F., Berkman, C.E.

To be published.

Macromolecule Content

Total Structure Weight: 84.13 kDa
Atom Count: 6,772
Modeled Residue Count: 694
Deposited Residue Count: 709
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate carboxypeptidase 2	A	709	Homo sapiens	Mutation(s): 0 Gene Names: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA EC: 3.4.17.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q04609 (Homo sapiens) Explore Q04609 Go to UniProtKB: Q04609
PHAROS: Q04609 GTEx: ENSG00000086205
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04609
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A	Go to GlyGen: Q04609-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T57 Query on T57 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	N-{6-[(4-fluorobenzoyl)amino]hexanoyl}-L-gamma-glutamyl-5-{[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]oxy}-L-norvaline C₂₈ H₄₀ F N₄ O₁₄ P IZLOSIXADNUSCM-ACRUOGEOSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
T57	BindingDB: 4JYW	IC50: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.181 (Depositor), 0.192 (DCC)
R-Value Work: 0.158 (Depositor), 0.172 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.625	α = 90
b = 130.326	β = 90
c = 158.305	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Barinka, C.

Revision History (Full details and data files)

Version 1.0: 2014-04-02
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary