9KZN | pdb_00009kzn

Crystal structure of Tom1 in complex with Tollip

PDB DOI: https://doi.org/10.2210/pdb9KZN/pdb

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

Deposited: 2024-12-11 Released: 2025-12-17
Deposition Author(s): Wang, Y.L., Gong, X.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.187 (Depositor), 0.187 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Tollip TBD coordinates uncanonical Parkin-dependent mitochondrial clearance

Wang, Y.L., Gong, X.Y.

To be published.

Macromolecule Content

Total Structure Weight: 14.74 kDa
Atom Count: 1,040
Modeled Residue Count: 118
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-interacting protein, Target of Myb1 membrane trafficking protein	A	129	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O60784 (Homo sapiens) Explore O60784 Go to UniProtKB: O60784
PHAROS: O60784 GTEx: ENSG00000100284
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.187 (Depositor), 0.187 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.271	α = 90
b = 43.271	β = 90
c = 59.477	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31800646

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.