7H5C | pdb_00007h5c

Crystal structure of endothiapepsin PN_cryo3 in complex with AC40075 at 100 K

PDB DOI: https://doi.org/10.2210/pdb7H5C/pdb
Deposition Group: G_1002290 | Explore G_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 (Depositor), 0.195 (DCC)
R-Value Work:
0.153 (Depositor), 0.153 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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

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

(2024) Acta Crystallogr D Struct Biol 80: 620-628

PubMed: 39052318 Search on PubMed
DOI: https://doi.org/10.1107/S2059798324006697
Primary Citation 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 frozen 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: 38.22 kDa
Atom Count: 2,934
Modeled Residue Count: 330
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 AB [auth A] SDF format, chain BA [auth A] SDF format, chain BB [auth A] SDF format, chain C [auth A] SDF format, chain CA [auth A] SDF format, chain CB [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain DB [auth A] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain EB [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain KA [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 QA [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth A] SDF format, chain W [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 YA [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [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 QA [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain W [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 YA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth A] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth A] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth A]	AA [auth A] AB [auth A] BA [auth A] BB [auth A] C [auth A] AA [auth A], AB [auth A], BA [auth A], BB [auth A], C [auth A], CA [auth A], CB [auth A], D [auth A], DA [auth A], DB [auth A], E [auth A], EA [auth A], EB [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], YA [auth A], Z [auth A], ZA [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [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 YA [auth A] Focus chain Z [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [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 YA [auth A] Focus chain Z [auth A] Focus chain ZA [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]