7QP3 | pdb_00007qp3

Pseudogymnoascus pannorum M36 protease without the propeptide

PDB DOI: https://doi.org/10.2210/pdb7QP3/pdb

Classification: RECOMBINATION
Organism(s): Pseudogymnoascus pannorum
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2021-12-30 Released: 2023-01-18
Deposition Author(s): Wilkens, C., Qiu, J., Meyer, A.S., Morth, J.P.
Funding Organization(s): Chinese Scholarship Council, Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.149 (Depositor), 0.148 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7QP3

This is version 1.2 of the entry. See complete history.

Literature

Phaeosphaeria nodorum M36 protease without the propeptide

Wilkens, C., Qiu, J., Meyer, A.S., Morth, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 42.94 kDa
Atom Count: 3,451
Modeled Residue Count: 391
Deposited Residue Count: 391
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular metalloproteinase	A	391	Pseudogymnoascus pannorum	Mutation(s): 0 EC: 3.4.24
UniProt
Find proteins for A0A1B8GTG7 (Pseudogymnoascus verrucosus) Explore A0A1B8GTG7 Go to UniProtKB: A0A1B8GTG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1B8GTG7
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE 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]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
A2G Query on A2G Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.149 (Depositor), 0.148 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.08	α = 90
b = 67.49	β = 90
c = 130.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
Coot	model building
PHASER	phasing
XDS	data scaling
XDS	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Scholarship Council		201806910049
Other government	Denmark	--

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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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.