9C0Y

Clathrin terminal domain complexed with Pitstop 2c

PDB DOI: https://doi.org/10.2210/pdb9C0Y/pdb

Classification: ENDOCYTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-28 Released: 2024-06-26
Deposition Author(s): Bulut, H., Horatscheck, A., Krauss, M., Santos, K.F., McCluskey, A., Wahl, C.W., Nazare, M., Haucke, V.
Funding Organization(s): Leibniz Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.206
R-Value Work: 0.184
R-Value Observed: 0.185

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

Acute inhibition of clathrin-mediated endocytosis by next-generation small molecule inhibitors of clathrin function

Horatscheck, A., Krauss, M., Bulut, H., Chambon, V., Zadah, M.S., Dransart, E., Peloza, K., Robertson, M.J., Santos, K.F., Miksche, S., Radetzky, S., von Kries, J.P., Wahl, M.C., McCluskey, M., Johannes, L., Haucke, V., Nazare, M.

To be published.

Macromolecule Content

Total Structure Weight: 42.45 kDa
Atom Count: 3,227
Modelled Residue Count: 358
Deposited Residue Count: 369
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clathrin heavy chain 1	A	369	Homo sapiens	Mutation(s): 0 Gene Names: CLTC, CLH17, CLTCL2, KIAA0034
UniProt & NIH Common Fund Data Resources
Find proteins for Q00610 (Homo sapiens) Explore Q00610 Go to UniProtKB: Q00610
PHAROS: Q00610 GTEx: ENSG00000141367
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00610
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ATR (Subject of Investigation/LOI) Query on A1ATR Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	N-{(5Z)-4-oxo-5-[(2-phenoxyphenyl)methylidene]-4,5-dihydro-1,3-thiazol-2-yl}naphthalene-2-sulfonamide C₂₆ H₁₈ N₂ O₄ S₂ UIPSKQQKIPOXRV-ULJHMMPZSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	I [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]