3T6I

Endothiapepsin in complex with an azepin derivative

PDB DOI: https://doi.org/10.2210/pdb3T6I/pdb

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

Deposited: 2011-07-28 Released: 2012-08-01
Deposition Author(s): Koester, H., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.149
R-Value Work: 0.129
R-Value Observed: 0.130

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Endothiapepsin in complex with an azepin derivative

Koester, H., Heine, A., Diederich, W.E., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 35.37 kDa
Atom Count: 2,903
Modelled Residue Count: 330
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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(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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NC8 Query on NC8 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(3R)-3-({(4-aminobenzyl)[(4-aminophenyl)acetyl]amino}methyl)-5-{[(4-bromobenzoyl)oxy]methyl}-2,3,4,7-tetrahydro-1H-azepinium C₃₀ H₃₄ Br N₄ O₃ ILVATMQGTNYMLQ-XMMPIXPASA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NC9 Query on NC9 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(3R)-3-({(4-aminobenzyl)[(4-aminophenyl)acetyl]amino}methyl)-5-(hydroxymethyl)-2,3,4,7-tetrahydro-1H-azepinium C₂₃ H₃₁ N₄ O₂ WRSLWDODYIRHLE-HXUWFJFHSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
Z82 Query on Z82 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	4-bromobenzoic acid C₇ H₅ Br O₂ TUXYZHVUPGXXQG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	G [auth A], H [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.149
R-Value Work: 0.129
R-Value Observed: 0.130
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.38	α = 90
b = 73.44	β = 109.96
c = 53.26	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-01

Deposition Author(s):

Koester, H.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2012-08-01
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3T6I

Endothiapepsin in complex with an azepin derivative

Endothiapepsin in complex with an azepin derivative

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)