3QGJ

1.3A Structure of alpha-Lytic Protease Bound to Ac-AlaAlaPro-Alanal

PDB DOI: https://doi.org/10.2210/pdb3QGJ/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Lysobacter enzymogenes
Mutation(s): No

Deposited: 2011-01-24 Released: 2012-02-01
Deposition Author(s): Everill, P., Meinke, G., Bohm, A., Bachovchin, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.192
R-Value Work: 0.167
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Substrate Binding Defines Ser195 Position in the Catalytic Triad of Serine Proteases, Not His57 protonation

Everill, P., Meinke, G., Bohm, A., Bachovchin, W.

To be published.

Macromolecule Content

Total Structure Weight: 41.87 kDa
Atom Count: 3,724
Modelled Residue Count: 406
Deposited Residue Count: 406
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-lytic protease	A, C	198	Lysobacter enzymogenes	Mutation(s): 0 EC: 3.4.21.12
UniProt
Find proteins for P00778 (Lysobacter enzymogenes) Explore P00778 Go to UniProtKB: P00778
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00778
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ac-AlaAlaPro-Alanal peptide	B, D	5	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TFA Query on TFA Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain T [auth C] SDF format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth C] MOL2 format, chain L [auth A]	L [auth A], M [auth A], N [auth A], T [auth C]	trifluoroacetic acid C₂ H F₃ O₂ DTQVDTLACAAQTR-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth C] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File 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 Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] 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 Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C]	H [auth A] I [auth A] J [auth A] K [auth A] Q [auth C] H [auth A], I [auth A], J [auth A], K [auth A], Q [auth C], R [auth C], S [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C]	E [auth A], F [auth A], G [auth A], O [auth C], P [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth C] Focus chain P [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001069 Query on PRD_001069	B, D	N-acetyl-L-alanyl-L-alanyl-N-[(2S)-1-hydroxypropan-2-yl]-L-prolinamide	Peptide-like / Inhibitor		Interactions Focus chain B Focus chain D Interactions & Density Focus chain B Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.192
R-Value Work: 0.167
R-Value Observed: 0.168
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.936	α = 90
b = 63.936	β = 90
c = 316.897	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-01
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2014-05-28
Changes: Data collection
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations

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Help and Resources

3QGJ

1.3A Structure of alpha-Lytic Protease Bound to Ac-AlaAlaPro-Alanal

Substrate Binding Defines Ser195 Position in the Catalytic Triad of Serine Proteases, Not His57 protonation

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2