9HLD | pdb_00009hld

TRPML1 in complex with compound 13

PDB DOI: https://doi.org/10.2210/pdb9HLD/pdb
EM Map EMD-52251: EMDB EMDataResource

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

Deposited: 2024-12-04 Released: 2025-06-04
Deposition Author(s): Reeks, J., Mahajan, P., Clark, M., Cowan, S.R., Di Daniel, E., Earl, C.P., Fisher, S., Holvey, R.S., Jackson, S.M., Lloyd-Evans, E., Morgillo, C.M., Mortenson, P.N., O'Reilly, M., Richardson, C.J., Schopf, P., Tams, D.M., Waller-Evans, H., Ward, S.E., Whibley, S., Williams, P.A., Johnson, C.N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Currently 9HLD does not have a validation slider image.

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

Literature

Enabling High Throughput Electron Cryo-microscopy for Structure-based Design

Reeks, J., Mahajan, P., Clark, M., Cowan, S.R., Di Daniel, E., Earl, C.P., Fisher, S., Holvey, R.S., Jackson, S.M., Lloyd-Evans, E., Morgillo, C.M., Mortenson, P.N., O'Reilly, M., Richardson, C.J., Schopf, P., Tams, D.M., Waller-Evans, H., Ward, S.E., Whibley, S., Williams, P.A., Johnson, C.N.

To be published.

Macromolecule Content

Total Structure Weight: 291.37 kDa
Atom Count: 15,832
Modeled Residue Count: 1,840
Deposited Residue Count: 2,512
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucolipin-1	A, B, C, D	628	Homo sapiens	Mutation(s): 0 Gene Names: MCOLN1, ML4, TRPML1, MSTP080
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZU1 (Homo sapiens) Explore Q9GZU1 Go to UniProtKB: Q9GZU1
PHAROS: Q9GZU1 GTEx: ENSG00000090674
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GZU1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q9GZU1-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	E, F, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EUJ Query on EUJ Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain V [auth B] SDF format, chain MA [auth D] SDF format, chain N [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A]	DA [auth C], MA [auth D], N [auth A], V [auth B]	(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate C₂₅ H₄₉ O₁₉ P₃ QXHVLVSULWMTCV-DICZBTHZSA-N		Interactions Focus chain DA [auth C] Focus chain MA [auth D] Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain MA [auth D] Focus chain N [auth A] Focus chain V [auth B]
A1IV6 (Subject of Investigation/LOI) Query on A1IV6 Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain X [auth B] SDF format, chain FA [auth C] SDF format, chain P [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain P [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain P [auth A]	FA [auth C], GA [auth D], P [auth A], X [auth B]	1-[(8R,9S,13S,14S,17S)-13-methyl-17-oxidanyl-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-3-yl]ethanone C₂₀ H₂₆ O₂ LURXOLBKAUTYIC-SLHNCBLASA-N		Interactions Focus chain FA [auth C] Focus chain GA [auth D] Focus chain P [auth A] Focus chain X [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth D] Focus chain P [auth A] Focus chain X [auth B]
8K6 Query on 8K6 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain T [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B]	BA [auth C], KA [auth D], L [auth A], T [auth B]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain KA [auth D] Focus chain L [auth A] Focus chain T [auth B] Interactions & Density Focus chain BA [auth C] Focus chain KA [auth D] Focus chain L [auth A] Focus chain T [auth B]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C]	IA [auth D], J [auth A], R [auth B], Z [auth C]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain IA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain AA [auth C] SDF format, chain S [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain S [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain S [auth B]	AA [auth C], JA [auth D], K [auth A], S [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain JA [auth D] Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain JA [auth D] Focus chain K [auth A] Focus chain S [auth B]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain Y [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth C]	HA [auth D], I [auth A], Q [auth B], Y [auth C]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain Y [auth C] Interactions & Density Focus chain HA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain Y [auth C]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain EA [auth C] SDF format, chain LA [auth D] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain M [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A]	CA [auth C] EA [auth C] LA [auth D] M [auth A] NA [auth D] CA [auth C], EA [auth C], LA [auth D], M [auth A], NA [auth D], O [auth A], U [auth B], W [auth B]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain EA [auth C] Focus chain LA [auth D] Focus chain M [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain U [auth B] Focus chain W [auth B] Interactions & Density Focus chain CA [auth C] Focus chain EA [auth C] Focus chain LA [auth D] Focus chain M [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain U [auth B] Focus chain W [auth B]