3V9M | pdb_00003v9m

Phospholipase ACII4 from Australian King Brown Snake

PDB DOI: https://doi.org/10.2210/pdb3V9M/pdb

Classification: HYDROLASE
Organism(s): Pseudechis australis
Mutation(s): No

Deposited: 2011-12-27 Released: 2013-02-13
Deposition Author(s): Guddat, L.W., Millers, E.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.225 (Depositor), 0.222 (DCC)
R-Value Work:
0.188 (Depositor), 0.184 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Mechanistic studies on the anticoagulant activity of a phospholipase A2 from the venom of the Australian King Brown Snake (Pseudechis australis)

Trabi, M., Millers, E.-K., Richards, R., Snelling, H., Keegan, R., Lavin, M.F., de Jersey, J., Guddat, L.W., Masci, P.

To be published.

Macromolecule Content

Total Structure Weight: 26.81 kDa
Atom Count: 2,173
Modeled Residue Count: 236
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 isozyme PA-11	A, B	118	Pseudechis australis	Mutation(s): 0 EC: 3.1.1.4
UniProt
Find proteins for P04056 (Pseudechis australis) Explore P04056 Go to UniProtKB: P04056
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04056
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] 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], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.225 (Depositor), 0.222 (DCC)
R-Value Work: 0.188 (Depositor), 0.184 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.38	α = 90
b = 82.38	β = 90
c = 28.9	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
PHENIX	refinement
CrystalClear	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Guddat, L.W.

Millers, E.K.

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

3V9M | pdb_00003v9m

Phospholipase ACII4 from Australian King Brown Snake

Literature

Mechanistic studies on the anticoagulant activity of a phospholipase A2 from the venom of the Australian King Brown Snake (Pseudechis australis)

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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