9M8Y | pdb_00009m8y

Cryo-EM structure of human OAT1 in complex with cefazolin

PDB DOI: https://doi.org/10.2210/pdb9M8Y/pdb
EM Map EMD-63724: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes MemProtMD

Deposited: 2025-03-13 Released: 2025-06-18
Deposition Author(s): Zhang, W., Zhang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9M8Y

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

Literature

Cryo-EM structure of human OAT1 in complex with cefazolin

Zhang, W., Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 57.58 kDa
Atom Count: 3,666
Modeled Residue Count: 490
Deposited Residue Count: 522
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Solute carrier family 22 member 6	A	522	Homo sapiens	Mutation(s): 0 Gene Names: SLC22A6, OAT1, PAHT Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q4U2R8 (Homo sapiens) Explore Q4U2R8 Go to UniProtKB: Q4U2R8
PHAROS: Q4U2R8 GTEx: ENSG00000197901
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4U2R8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X56 Query on X56 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Cefazolin C₁₄ H₁₄ N₈ O₄ S₃ MLYYVTUWGNIJIB-BXKDBHETSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-06-18
Type: Initial release

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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.