9F41

Crystal structure of the NTD domain from S. cerevisia Niemann-Pick type C protein NCR1 with cholesterol bound

PDB DOI: https://doi.org/10.2210/pdb9F41/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2024-04-26 Released: 2024-05-29
Deposition Author(s): Nel, L., Olesen, E., Frain, K.M., Pedersen, B.P.
Funding Organization(s): Danish Council for Independent Research, The Carlsberg Foundation, European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.260
R-Value Work: 0.226
R-Value Observed: 0.227

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and biochemical analysis of ligand binding in yeast Niemann-Pick type C 1-related protein

Jamecna, D., Thaysen, K., Nel, L., Olesen, E., Szomek, M., Frain, K.M., Langer, J., Pedersen, B.P., Wustner, D., Hoglinger, D.

To be published.

Macromolecule Content

Total Structure Weight: 127.95 kDa
Atom Count: 8,155
Modelled Residue Count: 888
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPC intracellular sterol transporter 1-related protein 1	A, B, C, D	248	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: NCR1, YPL006W
UniProt
Find proteins for Q12200 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12200 Go to UniProtKB: Q12200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12200
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q12200-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, N	7		N-Glycosylation	Interactions Focus chain E Focus chain N Interactions & Density Focus chain E Focus chain N
Glycosylation Resources
GlyTouCan: G91845HM GlyCosmos: G91845HM GlyGen: G91845HM

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, O	4		N-Glycosylation	Interactions Focus chain F Focus chain O Interactions & Density Focus chain F Focus chain O
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	9		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	6		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G47410OF GlyCosmos: G47410OF GlyGen: G47410OF

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, L [auth K]	5		N-Glycosylation	Interactions Focus chain I Focus chain L [auth K] Interactions & Density Focus chain I Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, M [auth L], P	4		N-Glycosylation	Interactions Focus chain J Focus chain M [auth L] Focus chain P Interactions & Density Focus chain J Focus chain M [auth L] Focus chain P
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth M]	6		N-Glycosylation	Interactions Focus chain K [auth M] Interactions & Density Focus chain K [auth M]
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain MA [auth C] SDF format, chain Q [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain Q [auth A]	BB [auth D], CA [auth B], MA [auth C], Q [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain BB [auth D] Focus chain CA [auth B] Focus chain MA [auth C] Focus chain Q [auth A] Interactions & Density Focus chain BB [auth D] Focus chain CA [auth B] Focus chain MA [auth C] Focus chain Q [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain V [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A]	T [auth A], V [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain T [auth A] Focus chain V [auth A] Interactions & Density Focus chain T [auth A] Focus chain V [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain W [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain W [auth A]	SA [auth C], TA [auth C], U [auth A], UA [auth C], W [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain W [auth A] Interactions & Density Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain W [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain PA [auth C] SDF format, chain S [auth A] SDF format, chain VA [auth C] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain PA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	EB [auth D] FB [auth D] IA [auth B] JA [auth B] JB [auth D] EB [auth D], FB [auth D], IA [auth B], JA [auth B], JB [auth D], PA [auth C], S [auth A], VA [auth C], X [auth A], Y [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EB [auth D] Focus chain FB [auth D] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain PA [auth C] Focus chain S [auth A] Focus chain VA [auth C] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain EB [auth D] Focus chain FB [auth D] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain PA [auth C] Focus chain S [auth A] Focus chain VA [auth C] Focus chain X [auth A] Focus chain Y [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth C] SDF format, chain BA [auth A] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain LA [auth B] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C]	AA [auth A] AB [auth C] BA [auth A] CB [auth D] DA [auth B] AA [auth A], AB [auth C], BA [auth A], CB [auth D], DA [auth B], DB [auth D], EA [auth B], FA [auth B], GA [auth B], GB [auth D], HA [auth B], HB [auth D], IB [auth D], KA [auth B], KB [auth D], LA [auth B], NA [auth C], OA [auth C], QA [auth C], R [auth A], RA [auth C], WA [auth C], XA [auth C], YA [auth C], Z [auth A], ZA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain LA [auth B] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain LA [auth B] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C]