8BO8

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with an inhibitor P17

PDB DOI: https://doi.org/10.2210/pdb8BO8/pdb

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

Deposited: 2022-11-15 Released: 2023-11-29
Deposition Author(s): Motlova, L., Barinka, C., Benesova, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.226
R-Value Work: 0.202
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with an inhibitor P17

Motlova, L., Barinka, C., Benesova, M.

To be published.

Macromolecule Content

Total Structure Weight: 84.55 kDa
Atom Count: 6,614
Modelled Residue Count: 693
Deposited Residue Count: 707
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate carboxypeptidase 2	A	707	Homo sapiens	Mutation(s): 0 Gene Names: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, F	3		N-Glycosylation	Interactions Focus chain B Focus chain F Interactions & Density Focus chain B Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	C	5		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QWF (Subject of Investigation/LOI) Query on QWF Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	(2~{S})-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-6-[[(~{E},2~{S})-5-phenyl-2-[[4-[[2-[4,7,10-tris(2-hydroxy-2-oxoethyl)-1,4,7,10-tetrazacyclododec-1-yl]ethanoylamino]methyl]cyclohexyl]carbonylamino]pent-4-enoyl]amino]hexan-2-yl]carbamoylamino]pentanedioic acid C₄₇ H₇₁ N₉ O₁₆ PDXVBYVTYTYYEQ-QMBVCIHYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [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 G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [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]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]