2G58

Crystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution

PDB DOI: https://doi.org/10.2210/pdb2G58/pdb

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

Deposited: 2006-02-22 Released: 2006-03-28
Deposition Author(s): Prem Kumar, R., Singh, N., Somvanshi, R.K., Ethayathulla, A.S., Dey, S., Sharma, S., Kaur, P., Perbandt, M., Betzel, C., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free: 0.157
R-Value Work: 0.133

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution

Prem Kumar, R., Singh, N., Somvanshi, R.K., Ethayathulla, A.S., Dey, S., Sharma, S., Kaur, P., Perbandt, M., Betzel, C., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 14.52 kDa
Atom Count: 1,394
Modelled Residue Count: 126
Deposited Residue Count: 126
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
(PHQ)IARS	B	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [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: 0.98 Å
R-Value Free: 0.157
R-Value Work: 0.133
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.588	α = 90
b = 52.588	β = 90
c = 47.848	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-03-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-03-28
Type: Initial release
Version 1.1: 2008-05-01
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: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Derived calculations, Source and taxonomy
Version 1.6: 2024-11-13
Changes: Structure summary