8VPL | pdb_00008vpl

Glutaminyl cyclase ApgG, diamond shape

PDB DOI: https://doi.org/10.2210/pdb8VPL/pdb

Classification: TRANSFERASE
Organism(s): Aspergillus flavus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-16 Released: 2025-06-18
Deposition Author(s): Nie, Q., Chang, C., Gao, Y., Gao, X.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.260 (Depositor), 0.260 (DCC)
R-Value Work:
0.240 (Depositor), 0.240 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Glutaminyl cyclase ApgG, diamond shape

Nie, Q., Chang, C., Gao, Y., Gao, X.

To be published.

Macromolecule Content

Total Structure Weight: 39.2 kDa
Atom Count: 2,731
Modeled Residue Count: 343
Deposited Residue Count: 353
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide hydrolase	A	353	Aspergillus flavus	Mutation(s): 0 Gene Names: F9C07_6934 EC: 3.4
UniProt
Find proteins for A0A5N6D8V5 (Aspergillus parasiticus) Explore A0A5N6D8V5 Go to UniProtKB: A0A5N6D8V5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5N6D8V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.260 (Depositor), 0.260 (DCC)
R-Value Work: 0.240 (Depositor), 0.240 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.266	α = 90
b = 70.266	β = 90
c = 145.174	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R23490

Revision History (Full details and data files)

Version 1.0: 2025-06-18
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.