3FG5 | pdb_00003fg5

Crystal structure determination of a ternary complex of phospholipase A2 with a pentapeptide FLSYK and Ajmaline at 2.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb3FG5/pdb

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

Deposited: 2008-12-05 Released: 2008-12-23
Deposition Author(s): Kumar, M., Kumar, S., Vikram, G., Singh, N., Sinha, M., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.227 (Depositor), 0.220 (DCC)
R-Value Work:
0.188 (Depositor), 0.180 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure determination of a ternary complex of phospholipase A2 with a pentapeptide FLSYK and Ajmaline at 2.5 A resolution

Kumar, M., Kumar, S., Vikram, G., Singh, N., Sinha, M., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 14.59 kDa
Atom Count: 1,073
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
Group II Phospholipase A2	A	121	Daboia russelii pulchella	Mutation(s): 0 EC: 3.1.1.4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
pentapeptide FLSYK	B [auth C]	5	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AJM Query on AJM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	AJMALINE C₁₈ H₂₂ N₂ O₂ CFEPCEVMXPTZPJ-OGDRVKPDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.227 (Depositor), 0.220 (DCC)
R-Value Work: 0.188 (Depositor), 0.180 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.949	α = 90
b = 52.949	β = 90
c = 48.445	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary