21NW | pdb_000021nw

Cryo-EM structure of human Lipid Phosphate Phosphatase 2

PDB DOI: https://doi.org/10.2210/pdb21NW/pdb
EM Map EMD-67854: EMDB EMDataResource

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

Deposited: 2025-12-21 Released: 2026-05-06
Deposition Author(s): Wang, W.Y., Han, L.
Funding Organization(s): National Key R&D Program of China, National Natural Science Foundation of China (NSFC), Fundamental Research Funds for the Central Universities

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of human Lipid Phosphate Phosphatase 2

Wang, W.Y., Han, L.

To be published.

Macromolecule Content

Total Structure Weight: 134.35 kDa
Atom Count: 7,604
Modeled Residue Count: 940
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipid phosphatase 2	A, B, C, D	288	Homo sapiens	Mutation(s): 0 Gene Names: PLPP2, LPP2, PPAP2C EC: 3.1.3 (PDB Primary Data), 3.1.3.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43688 (Homo sapiens) Explore O43688 Go to UniProtKB: O43688
PHAROS: O43688 GTEx: ENSG00000141934
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43688
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: O43688-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPL Query on CPL 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]	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₂ H₈₀ N O₈ P JLPULHDHAOZNQI-ZTIMHPMXSA-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]
NAG (Subject of Investigation/LOI) Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-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: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Wang, W.Y.

Han, L.

Funding Organization	Location	Grant Number
National Key R&D Program of China	China	2024YFA1306103
National Natural Science Foundation of China (NSFC)	China	32370766, 82573060
Fundamental Research Funds for the Central Universities	China	2042025kf0001