7H5D

Crystal structure of endothiapepsin PN_cryo1 in complex with AC40075 at 100 K

PDB DOI: https://doi.org/10.2210/pdb7H5D/pdb
Deposition Group: G_1002290 ExploreG_1002290

Classification: HYDROLASE
Organism(s): Cryphonectria parasitica
Mutation(s): No

Deposited: 2024-04-10 Released: 2024-08-07
Deposition Author(s): Huang, C.-Y., Aumonier, S., Olieric, V., Wang, M.
Funding Organization(s): Swiss National Science Foundation, H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.199
R-Value Work: 0.160
R-Value Observed: 0.162

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryocooled crystals.

Huang, C.Y., Aumonier, S., Olieric, V., Wang, M.

(2024) Acta Crystallogr D Struct Biol

PubMed: 39052318 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2059798324006697
Primary Citation of Related Structures:
7H56, 7H57, 7H58, 7H59, 7H5A, 7H5B, 7H5C, 7H5D, 7H5E, 7H5F, 7H5G, 7H5H, 7H5I, 7H5J, 7H5K, 7H5L, 7H5M, 7H5N, 7H5O, 7H5P, 7H5Q, 7H5R, 7H5S, 7H5T, 7H5U, 7H5V, 7H5W, 7H5X, 7H5Y, 7H5Z, 9FX4, 9FX5, 9FX6, 9FX7

PubMed Abstract:
Advances in structural biology have relied heavily on synchrotron cryo-crystallography and cryogenic electron microscopy to elucidate biological processes and for drug discovery. However, disparities between cryogenic and room-temperature (RT) crystal structures pose challenges. Here, Cryo2RT, a high-throughput RT data-collection method from cryo-cooled crystals that leverages the cryo-crystallography workflow, is introduced. Tested on endothiapepsin crystals with four soaked fragments, thaumatin and SARS-CoV-2 3CL ^pro, Cryo2RT reveals unique ligand-binding poses, offers a comparable throughput to cryo-crystallography and eases the exploration of structural dynamics at various temperatures.

Organizational Affiliation

Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland.

Macromolecule Content

Total Structure Weight: 37.68 kDa
Atom Count: 2,912
Modelled Residue Count: 330
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A	330	Cryphonectria parasitica	Mutation(s): 0 EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838 Go to UniProtKB: P11838
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11838
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EMR (Subject of Investigation/LOI) Query on EMR Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	N-AMINOETHYLMORPHOLINE C₆ H₁₄ N₂ O RWIVICVCHVMHMU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain C [auth A] SDF format, chain DA [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth A] SDF format, chain Q [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain X [auth A] SDF format, chain XA [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain CA [auth A] SDF format, chain D [auth A] SDF format, chain EA [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth A] SDF format, chain QA [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain TA [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A]	AA [auth A] BA [auth A] C [auth A] CA [auth A] D [auth A] AA [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], RA [auth A], S [auth A], SA [auth A], T [auth A], TA [auth A], U [auth A], UA [auth A], V [auth A], VA [auth A], W [auth A], WA [auth A], X [auth A], XA [auth A], Y [auth A], Z [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain SA [auth A] Focus chain T [auth A] Focus chain TA [auth A] Focus chain U [auth A] Focus chain UA [auth A] Focus chain V [auth A] Focus chain VA [auth A] Focus chain W [auth A] Focus chain WA [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain SA [auth A] Focus chain T [auth A] Focus chain TA [auth A] Focus chain U [auth A] Focus chain UA [auth A] Focus chain V [auth A] Focus chain VA [auth A] Focus chain W [auth A] Focus chain WA [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]