4QNN

Crystal Structure of phospholipase A 1 from hornet(Vespa basalis) venom

PDB DOI: https://doi.org/10.2210/pdb4QNN/pdb

Classification: HYDROLASE
Organism(s): Vespa basalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-18 Released: 2015-06-24
Deposition Author(s): Chuang, C.Y., Ko, T.P., Wang, A.H.J., Hou, M.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.279
R-Value Work: 0.204
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of phospholipase A 1 from hornet(Vespa basalis) venom

Chuang, C.Y., Ko, T.P., Wang, A.H.J., Hou, M.H.

To be published.

Macromolecule Content

Total Structure Weight: 134.37 kDa
Atom Count: 9,672
Modelled Residue Count: 1,188
Deposited Residue Count: 1,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A 1 from hornet(Vespa basalis) venom	A, B, C, D	300	Vespa basalis	Mutation(s): 0 EC: 3.1.1.32
UniProt
Find proteins for A0A0M3KKW3 (Vespa basalis) Explore A0A0M3KKW3 Go to UniProtKB: A0A0M3KKW3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M3KKW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain J [auth A] SDF format, chain W [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain W [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain W [auth B]	BA [auth C], J [auth A], W [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain J [auth A] Focus chain W [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] CA [auth D] DA [auth D] E [auth A] EA [auth D] AA [auth C], CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], X [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.279
R-Value Work: 0.204
R-Value Observed: 0.204
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.276	α = 107.14
b = 70.147	β = 109.99
c = 81.724	γ = 100.9

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2018-03-07
Changes: Data collection
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary