3GKI

NPC1(NTD):cholesterol

• PDB DOI: https://doi.org/10.2210/pdb3GKI/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2009-03-10 Released: 2009-07-14 
• Deposition Author(s): Kwon, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.77 kDa 
• Atom Count: 1,921 
• Modelled Residue Count: 225 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Niemann-Pick C1 protein	A	232	Homo sapiens	Mutation(s): 3  Gene Names: NPC1
UniProt & NIH Common Fund Data Resources
Find proteins for O15118 (Homo sapiens) Explore O15118  Go to UniProtKB:  O15118
PHAROS:  O15118 GTEx:  ENSG00000141458

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	D [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.691	α = 90
b = 65.691	β = 90
c = 82.367	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Kwon, H.J.

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary