3GKJ
NPC1D(NTD):25hydroxycholesterol
- PDB DOI: https://doi.org/10.2210/pdb3GKJ/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2009-03-10 Released: 2009-07-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.203 
- R-Value Work: 0.175 
- R-Value Observed: 0.177 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Niemann-Pick C1 protein | 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  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O15118 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HC3 Query on HC3 | D [auth A] | 25-HYDROXYCHOLESTEROL C27 H46 O2 INBGSXNNRGWLJU-ZHHJOTBYSA-N | |||
NAG Query on 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: 1.60 Å
- R-Value Free: 0.203 
- R-Value Work: 0.175 
- R-Value Observed: 0.177 
- Space Group: P 64
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 65.926 | α = 90 |
b = 65.926 | β = 90 |
c = 82.988 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
Entry History 
Deposition Data
- Released Date: 2009-07-14  Deposition Author(s): Kwon, H.J.
Revision History (Full details and data files)
- 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