1SQZ | pdb_00001sqz

Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between Group II Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution

PDB DOI: https://doi.org/10.2210/pdb1SQZ/pdb

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

Deposited: 2004-03-22 Released: 2004-04-13
Deposition Author(s): Singh, N., Prem Kumar, R., Somvanshi, R.K., Bilgrami, S., Ethayathulla, A.S., Sharma, S., Dey, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.217 (Depositor)
R-Value Work:
0.209 (Depositor)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between GroupII Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution

Singh, N., Prem Kumar, R., Somvanshi, R.K., Bilgrami, S., Ethayathulla, A.S., Sharma, S., Dey, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 14.52 kDa
Atom Count: 1,300
Modeled Residue Count: 126
Deposited Residue Count: 126
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2	A	121	Daboia russelii russelii	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
synthetic peptide	B	5	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 E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000335 Query on PRD_000335	B	DEHYDRO-ILE-ALA-ARG-SER	Peptide-like / Inhibitor		Interactions Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.217 (Depositor)
R-Value Work: 0.209 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.549	α = 90
b = 52.549	β = 90
c = 47.833	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-04-13
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2012-12-12
Changes: Other
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-06
Changes: Structure summary