9AYI | pdb_00009ayi

Human malic enzyme 2 cofactor complex at 1.89 Angstrom.

PDB DOI: https://doi.org/10.2210/pdb9AYI/pdb

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

Deposited: 2024-03-07 Released: 2025-03-12
Deposition Author(s): Krinkel, B.A., Squire, C.J., Loomes, K.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.201 (Depositor), 0.207 (DCC)
R-Value Work:
0.177 (Depositor), 0.185 (DCC)
R-Value Observed:
0.178 (Depositor)

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

Human malic enzyme 2 complex with inhibitor NPD-389

Krinkel, B.A., Squire, C.J., Loomes, K.M.

To be published.

Macromolecule Content

Total Structure Weight: 265.23 kDa
Atom Count: 20,060
Modelled Residue Count: 2,209
Deposited Residue Count: 2,300
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent malic enzyme, mitochondrial	A, B, C, D	575	Homo sapiens	Mutation(s): 0 Gene Names: ME2 EC: 1.1.1.38
UniProt & NIH Common Fund Data Resources
Find proteins for P23368 (Homo sapiens) Explore P23368 Go to UniProtKB: P23368
PHAROS: P23368 GTEx: ENSG00000082212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23368
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain M [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain M [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain M [auth B]	AA [auth D] E [auth A] I [auth A] M [auth B] P [auth B] AA [auth D], E [auth A], I [auth A], M [auth B], P [auth B], U [auth C], V [auth C], Y [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D]	K [auth A], N [auth B], R [auth C], W [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain W [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth D]	F [auth A], G [auth A], O [auth B], S [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	H [auth A], L [auth B], T [auth C], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain X [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B]	J [auth A], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B]