2RD4 | pdb_00002rd4

Design of specific inhibitors of Phospholipase A2: Crystal structure of the complex of phospholipase A2 with pentapeptide Leu-Val-Phe-Phe-Ala at 2.9 A resolution

PDB DOI: https://doi.org/10.2210/pdb2RD4/pdb

Classification: HYDROLASE
Organism(s): Naja sagittifera
Mutation(s): No

Deposited: 2007-09-21 Released: 2007-10-09
Deposition Author(s): Mirza, Z., Kaur, A., Singh, N., Sinha, M., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free:
0.274 (Depositor)
R-Value Work:
0.251 (Depositor)
R-Value Observed:
0.258 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Design of specific inhibitors of Phospholipase A2: Crystal structure of the complex of phospholipase A2 with pentapeptide Leu-Val-Phe-Phe-Ala at 2.9 A resolution

Mirza, Z., Kaur, A., Singh, N., Sinha, M., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 27.19 kDa
Atom Count: 1,940
Modeled Residue Count: 243
Deposited Residue Count: 243
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 isoform 1	A	119	Naja sagittifera	Mutation(s): 0 EC: 3.1.1.4
UniProt
Find proteins for P60043 (Naja sagittifera) Explore P60043 Go to UniProtKB: P60043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60043
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 isoform 2	B	119	Naja sagittifera	Mutation(s): 0 EC: 3.1.1.4
UniProt
Find proteins for P60044 (Naja sagittifera) Explore P60044 Go to UniProtKB: P60044
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60044
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
pentapeptide inhibitor	C	5	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free: 0.274 (Depositor)
R-Value Work: 0.251 (Depositor)
R-Value Observed: 0.258 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.54	α = 90
b = 65.54	β = 90
c = 58.551	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
CNS	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-10-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-31
Changes: Experimental preparation
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary