2FNX | pdb_00002fnx

Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2): Crystal Structure of the Complex of PLA2 with a Highly Potent Peptide Val-Ile-Ala-Lys at 2.7A Resolution

PDB DOI: https://doi.org/10.2210/pdb2FNX/pdb

Classification: HYDROLASE
Organism(s): Daboia russelii pulchella
Mutation(s): No

Deposited: 2006-01-11 Released: 2006-01-24
Deposition Author(s): Singh, N., Srivastava, P., Sharma, S., Dey, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.231 (Depositor)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2): Crystal Structure of the Complex of PLA2 with a Highly Potent Peptide Val-Ile-Ala-Lys at 2.7A Resolution

Singh, N., Srivastava, P., Sharma, S., Dey, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 14.16 kDa
Atom Count: 1,034
Modeled Residue Count: 125
Deposited Residue Count: 125
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 VRV-PL-VIIIa	A	121	Daboia russelii pulchella	Mutation(s): 0 EC: 3.1.1.4
UniProt
Find proteins for P59071 (Daboia russelii) Explore P59071 Go to UniProtKB: P59071
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59071
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor peptide	B [auth P]	4	N/A	Mutation(s): 0

Small Molecules

Ligands 1 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] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.231 (Depositor)
R-Value Work: 0.189 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.06	α = 90
b = 53.06	β = 90
c = 48.524	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-01-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.