3DBK | pdb_00003dbk

Pseudomonas aeruginosa elastase with phosphoramidon

• PDB DOI: https://doi.org/10.2210/pdb3DBK/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Mutation(s): No 


• Deposited: 2008-06-01 Released: 2009-07-07 
• Deposition Author(s): McKay, D.B., Overgaard, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structure of the Elastase of Pseudomonas aeruginosa Complexed with Phosphoramidon

Overgaard, M.T., McKay, D.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.11 kDa 
• Atom Count: 2,747 
• Modeled Residue Count: 298 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elastase	A	301	Pseudomonas aeruginosa	Mutation(s): 0  EC: 3.4.24.26
UniProt
Find proteins for P14756 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P14756  Go to UniProtKB:  P14756

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RDF	G [auth A]	N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN C23 H34 N3 O10 P ZPHBZEQOLSRPAK-XLCYBJAPSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RDF	BindingDB:  3DBK	Ki: 57 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000638 (RDF)	G [auth A]	PHOSPHORAMIDON	Glycopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44	α = 90
b = 50.75	β = 90
c = 121.51	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): McKay, D.B., Overgaard, M.T.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-03-13
  Changes: Source and taxonomy
• Version 1.5: 2024-11-20
  Changes: Structure summary