4LP9 | pdb_00004lp9

Endothiapepsin complexed with Phe-reduced-Tyr peptide.

PDB DOI: https://doi.org/10.2210/pdb4LP9/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Cryphonectria parasitica
Mutation(s): No

Deposited: 2013-07-15 Released: 2014-01-15
Deposition Author(s): Guo, J., Cooper, J.B., Wood, S.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.165 (Depositor), 0.166 (DCC)
R-Value Work:
0.123 (Depositor), 0.122 (DCC)
R-Value Observed:
0.125 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

The structure of endothiapepsin complexed with a Phe-Tyr reduced-bond inhibitor at 1.35 angstrom resolution.

Guo, J., Cooper, J.B., Wood, S.P.

(2014) Acta Crystallogr D Biol Crystallogr 70: 30-33

PubMed: 24419612 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X13032974
Primary Citation Related Structures:
4LP9

PubMed Abstract:
Endothiapepsin is a typical member of the aspartic proteinase family. The catalytic mechanism of this family is attributed to two conserved catalytic aspartate residues, which coordinate the hydrolysis of a peptide bond. An oligopeptide inhibitor (IC50 = 0.62 µM) based on a reduced-bond transition-state inhibitor of mucorpepsin was co-crystallized with endothiapepsin and the crystal structure of the enzyme-inhibitor complex was determined at 1.35 Å resolution. A total of 12 hydrogen bonds between the inhibitor and the active-site residues were identified. The resulting structure demonstrates a number of novel subsite interactions in the active-site cleft.

Organizational Affiliation

Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England.

Macromolecule Content

Total Structure Weight: 35.65 kDa
Atom Count: 2,853
Modeled Residue Count: 337
Deposited Residue Count: 337
Unique protein chains: 2

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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro	B [auth I]	7	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain G [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001157 Query on PRD_001157	B [auth I]	Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro	Peptide-like / Inhibitor		Interactions Focus chain B [auth I] Interactions & Density Focus chain B [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.165 (Depositor), 0.166 (DCC)
R-Value Work: 0.123 (Depositor), 0.122 (DCC)
R-Value Observed: 0.125 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.62	α = 90
b = 72.787	β = 108.54
c = 45.113	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
FFT	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
FFT	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Guo, J.

Cooper, J.B.

Wood, S.P.

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2014-02-19
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2024-11-20
Changes: Structure summary