4X91

Crystal structure of Lysosomal Phospholipase A2 in complex with Isopropyl dodec-11-enylfluorophosphonate (IDFP)

PDB DOI: https://doi.org/10.2210/pdb4X91/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2014-12-11 Released: 2015-03-11
Deposition Author(s): Glukhova, A., Tesmer, J.J.G.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.214
R-Value Work: 0.183
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 179.92 kDa
Atom Count: 13,227
Modelled Residue Count: 1,504
Deposited Residue Count: 1,520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Group XV phospholipase A2	A, B, C, D	380	Homo sapiens	Mutation(s): 0 Gene Names: PLA2G15, LYPLA3, UNQ341/PRO540 EC: 2.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NCC3 (Homo sapiens) Explore Q8NCC3 Go to UniProtKB: Q8NCC3
PHAROS: Q8NCC3 GTEx: ENSG00000103066
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NCC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TO4 (Subject of Investigation/LOI) Query on TO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain I [auth A] SDF format, chain OA [auth D] SDF format, chain U [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain U [auth B]	EA [auth C], I [auth A], OA [auth D], U [auth B]	propan-2-yl (R)-dodec-11-en-1-ylphosphonofluoridate C₁₅ H₃₀ F O₂ P HAGAHLUSUUTRJV-LJQANCHMSA-N		Interactions Focus chain EA [auth C] Focus chain I [auth A] Focus chain OA [auth D] Focus chain U [auth B] Interactions & Density Focus chain EA [auth C] Focus chain I [auth A] Focus chain OA [auth D] Focus chain U [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain J [auth A] SDF format, chain PA [auth D] SDF format, chain V [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain V [auth B]	FA [auth C], J [auth A], PA [auth D], V [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain J [auth A] Focus chain PA [auth D] Focus chain V [auth B] Interactions & Density Focus chain FA [auth C] Focus chain J [auth A] Focus chain PA [auth D] Focus chain V [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] E [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], KA [auth D], LA [auth D], MA [auth D], NA [auth D], Q [auth B], R [auth B], S [auth B], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain SA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth C]	IA [auth C] JA [auth C] O [auth A] P [auth A] SA [auth D] IA [auth C], JA [auth C], O [auth A], P [auth A], SA [auth D], Y [auth B], Z [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain IA [auth C] Focus chain JA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain SA [auth D] Focus chain Y [auth B] Focus chain Z [auth C] Interactions & Density Focus chain IA [auth C] Focus chain JA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain SA [auth D] Focus chain Y [auth B] Focus chain Z [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	GA [auth C] HA [auth C] K [auth A] L [auth A] M [auth A] GA [auth C], HA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], QA [auth D], RA [auth D], W [auth B], X [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.214
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.83	α = 79.08
b = 90.172	β = 88.88
c = 99.345	γ = 89.11

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
SCALEPACK	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction
Aimless	data scaling
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-03-11

Deposition Author(s):

Glukhova, A.

Tesmer, J.J.G.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL086865

Revision History (Full details and data files)

Version 1.0: 2015-03-11
Type: Initial release
Version 1.1: 2015-03-18
Changes: Database references
Version 1.2: 2017-09-13
Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy
Version 1.3: 2017-11-22
Changes: Refinement description
Version 1.4: 2019-12-04
Changes: Author supporting evidence
Version 2.0: 2020-04-08
Type: Coordinate replacement
Reason: Ligand identity
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary