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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.203 (Depositor), 0.244 (DCC)
R-Value Work:
0.183 (Depositor)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure of the Elastase of Pseudomonas aeruginosa Complexed with Phosphoramidon

Overgaard, M.T., McKay, D.B.

To be published.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14756
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RDF Query on RDF Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN C₂₃ H₃₄ N₃ O₁₀ P ZPHBZEQOLSRPAK-XLCYBJAPSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.203 (Depositor), 0.244 (DCC)
R-Value Work: 0.183 (Depositor)
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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

McKay, D.B.

Overgaard, M.T.

Revision History (Full details and data files)

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