7ADG | pdb_00007adg

Cocktail experiment G: fragments 216 and 338 at 90 mM concentration in complex with Endothiapepsin

PDB DOI: https://doi.org/10.2210/pdb7ADG/pdb

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

Deposited: 2020-09-14 Released: 2021-10-06
Deposition Author(s): Hassaan, E., Klebe, G., Heine, A., Schiebel, J., Koester, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free:
0.144 (Depositor), 0.143 (DCC)
R-Value Work:
0.126 (Depositor), 0.126 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Comparison of Cocktail Screening in X-Ray Crystallography vs NMR

Hassaan, E., Klebe, G., Heine, A., Schiebel, J., Koester, H.

To be published.

Macromolecule Content

Total Structure Weight: 44.23 kDa
Atom Count: 2,934
Modeled Residue Count: 330
Deposited Residue Count: 419
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A	419	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
483 (Subject of Investigation/LOI) Query on 483 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]	2-(1H-imidazol-1-yl)-N-(trans-4-methylcyclohexyl)acetamide C₁₂ H₁₉ N₃ O PKHDTDLLHJFDKS-XYPYZODXSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
8NE (Subject of Investigation/LOI) Query on 8NE 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]	[azanyl-[4-(trifluoromethyl)phenyl]methylidene]azanium C₈ H₈ F₃ N₂ XFLGYXVBXUAGQV-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DMS Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-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]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]