3CBI | pdb_00003cbi

Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution

PDB DOI: https://doi.org/10.2210/pdb3CBI/pdb

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

Deposited: 2008-02-22 Released: 2008-03-11
Deposition Author(s): Kumar, S., Vikram, G., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.250 (Depositor), 0.240 (DCC)
R-Value Work:
0.228 (Depositor), 0.210 (DCC)

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 of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution

Kumar, S., Vikram, G., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 56.32 kDa
Atom Count: 3,904
Modeled Residue Count: 484
Deposited Residue Count: 484
Unique protein chains: 1

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, B, C, D	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AJM Query on AJM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	AJMALINE C₁₈ H₂₂ N₂ O₂ CFEPCEVMXPTZPJ-OGDRVKPDSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
ANN Query on ANN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	4-METHOXYBENZOIC ACID C₈ H₈ O₃ ZEYHEAKUIGZSGI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.250 (Depositor), 0.240 (DCC)
R-Value Work: 0.228 (Depositor), 0.210 (DCC)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.799	α = 90
b = 108.799	β = 90
c = 43.339	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	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: 2008-03-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-03-11
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: 2024-11-06
Changes: Structure summary

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Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution

Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3CBI | pdb_00003cbi