4FGA | pdb_00004fga

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 Å
R-Value Free:
0.243 (Depositor), 0.263 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 124
Deposited Residue Count: 124
Unique protein chains: 2

Macromolecules

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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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AYK	B [auth P]	3	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.243 (Depositor), 0.263 (DCC)
R-Value Work: 0.200 (Depositor), 0.199 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	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

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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.