9L76 | pdb_00009l76

Structures and mechanism of the nicotinamide nucleotide transhydrogenase from E. coli

PDB DOI: https://doi.org/10.2210/pdb9L76/pdb
EM Map EMD-62870: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-25 Released: 2026-01-07
Deposition Author(s): Zhu, J., Zhang, K., Gennis, R.B., Li, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9L76

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

Literature

Structures and mechanism of the nicotinamide nucleotide transhydrogenase from E. coli

Zhu, J., Zhang, K., Gennis, R.B., Li, J.

To be published.

Macromolecule Content

Total Structure Weight: 123.82 kDa
Atom Count: 8,604
Modeled Residue Count: 1,140
Deposited Residue Count: 1,140
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P) transhydrogenase subunit alpha	A [auth B], C [auth D]	108	Escherichia coli K-12	Mutation(s): 0 Gene Names: pntA, b1603, JW1595 EC: 7.1.1.1
UniProt
Find proteins for P07001 (Escherichia coli (strain K12)) Explore P07001 Go to UniProtKB: P07001
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07001
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P) transhydrogenase subunit beta	B [auth C], D [auth A]	462	Escherichia coli K-12	Mutation(s): 0 Gene Names: pntB, b1602, JW1594 EC: 7.1.1.1
UniProt
Find proteins for P0AB67 (Escherichia coli (strain K12)) Explore P0AB67 Go to UniProtKB: P0AB67
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AB67
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PKZ (Subject of Investigation/LOI) Query on PKZ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth C]	F [auth C], G [auth A]	Palmitoyl-CoA C₃₇ H₆₆ N₇ O₁₇ P₃ S MNBKLUUYKPBKDU-BBECNAHFSA-N		Interactions Focus chain F [auth C] Focus chain G [auth A] Interactions & Density Focus chain F [auth C] Focus chain G [auth A]
PC1 (Subject of Investigation/LOI) Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32201038

Revision History (Full details and data files)

Version 1.0: 2026-01-07
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.