4FGA

Design of peptide inhibitors of group II phospholipase A2: Crystal structure of the complex of phospholipsae A2 with a designed tripeptide, Ala- Tyr- Lys at 2.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb4FGA/pdb

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

Deposited: 2012-06-04 Released: 2012-06-27
Deposition Author(s): Shukla, P.K., Sinha, M., Dey, S., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free:
0.243 (Depositor), 0.260 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Design of peptide inhibitors of group II phospholipase A2: Crystal structure of the complex of phospholipsae A2 with a designed tripeptide, Ala- Tyr- Lys at 2.3 A resolution

Shukla, P.K., Sinha, M., Dey, S., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 14.01 kDa
Atom Count: 1,069
Modelled Residue Count: 124
Deposited Residue Count: 124
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
AYK	B [auth P]	3	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free: 0.243 (Depositor), 0.260 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( ? )	Angle ( ? )
a = 53.166	α = 90
b = 53.166	β = 90
c = 48.548	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-27
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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.