9F40

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

PDB DOI: https://doi.org/10.2210/pdb9F40/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: 2.44 Å
R-Value Free: 0.257
R-Value Work: 0.214
R-Value Observed: 0.216

Starting Model: experimental
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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., Frain, K.M., Szomek, M., Langer, J., Pedersen, B.P., Wustner, D., Hoglinger, D.

To be published.

Macromolecule Content

Total Structure Weight: 128.16 kDa
Atom Count: 8,163
Modelled Residue Count: 888
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

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(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

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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-(1-3)]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: G16404YH GlyCosmos: G16404YH GlyGen: G16404YH

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-(1-3)-[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	G	6		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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, K	6		N-Glycosylation	Interactions Focus chain H Focus chain K Interactions & Density Focus chain H Focus chain K
Glycosylation Resources
GlyTouCan: G47410OF GlyCosmos: G47410OF GlyGen: G47410OF

Entity ID: 6
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	I, J, P	4		N-Glycosylation	Interactions Focus chain I Focus chain J Focus chain P Interactions & Density Focus chain I Focus chain J Focus chain P
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 7
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	L	5		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	3		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ERG (Subject of Investigation/LOI) Query on ERG Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain OB [auth D] SDF format, chain Q [auth A] SDF format, chain UA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain UA [auth C]	FA [auth B], OB [auth D], Q [auth A], UA [auth C]	ERGOSTEROL C₂₈ H₄₄ O DNVPQKQSNYMLRS-APGDWVJJSA-N		Interactions Focus chain FA [auth B] Focus chain OB [auth D] Focus chain Q [auth A] Focus chain UA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain OB [auth D] Focus chain Q [auth A] Focus chain UA [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain TB [auth D] SDF format, chain W [auth A] SDF format, chain Z [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain TB [auth D] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth A]	AB [auth C] BB [auth C] CB [auth C] DA [auth A] DB [auth C] AB [auth C], BB [auth C], CB [auth C], DA [auth A], DB [auth C], LA [auth B], MA [auth B], NA [auth B], OA [auth B], TB [auth D], W [auth A], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain TB [auth D] Focus chain W [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain TB [auth D] Focus chain W [auth A] Focus chain Z [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain GA [auth B] SDF format, chain MB [auth C] SDF format, chain PB [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain TA [auth B] SDF format, chain VA [auth C] SDF format, chain ZB [auth D] MOL2 format, chain EA [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain PB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain ZB [auth D]	EA [auth A] GA [auth B] MB [auth C] PB [auth D] R [auth A] EA [auth A], GA [auth B], MB [auth C], PB [auth D], R [auth A], S [auth A], TA [auth B], VA [auth C], ZB [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth A] Focus chain GA [auth B] Focus chain MB [auth C] Focus chain PB [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth B] Focus chain VA [auth C] Focus chain ZB [auth D] Interactions & Density Focus chain EA [auth A] Focus chain GA [auth B] Focus chain MB [auth C] Focus chain PB [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth B] Focus chain VA [auth C] Focus chain ZB [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AC [auth D] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain LB [auth C] SDF format, chain NB [auth C] SDF format, chain QB [auth D] SDF format, chain RA [auth B] SDF format, chain RB [auth D] SDF format, chain SA [auth B] SDF format, chain SB [auth D] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VB [auth D] SDF format, chain WA [auth C] SDF format, chain WB [auth D] SDF format, chain XA [auth C] SDF format, chain XB [auth D] SDF format, chain YA [auth C] SDF format, chain YB [auth D] SDF format, chain ZA [auth C] MOL2 format, chain AC [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain QB [auth D] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain WA [auth C] MOL2 format, chain WB [auth D] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth D] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth D] MOL2 format, chain ZA [auth C]	AC [auth D] BA [auth A] CA [auth A] HA [auth B] HB [auth C] AC [auth D], BA [auth A], CA [auth A], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LB [auth C], NB [auth C], QB [auth D], RA [auth B], RB [auth D], SA [auth B], SB [auth D], T [auth A], U [auth A], V [auth A], VB [auth D], WA [auth C], WB [auth D], XA [auth C], XB [auth D], YA [auth C], YB [auth D], ZA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AC [auth D] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain NB [auth C] Focus chain QB [auth D] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VB [auth D] Focus chain WA [auth C] Focus chain WB [auth D] Focus chain XA [auth C] Focus chain XB [auth D] Focus chain YA [auth C] Focus chain YB [auth D] Focus chain ZA [auth C] Interactions & Density Focus chain AC [auth D] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain NB [auth C] Focus chain QB [auth D] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain VB [auth D] Focus chain WA [auth C] Focus chain WB [auth D] Focus chain XA [auth C] Focus chain XB [auth D] Focus chain YA [auth C] Focus chain YB [auth D] Focus chain ZA [auth C]
CCN Query on CCN Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain UB [auth D] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain UB [auth D] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	AA [auth A] EB [auth C] FB [auth C] GB [auth C] PA [auth B] AA [auth A], EB [auth C], FB [auth C], GB [auth C], PA [auth B], QA [auth B], UB [auth D], X [auth A], Y [auth A]	ACETONITRILE C₂ H₃ N WEVYAHXRMPXWCK-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain UB [auth D] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth A] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain UB [auth D] Focus chain X [auth A] Focus chain Y [auth A]