8KIB

NADP+-dependent cytosolic isocitrate dehydrogenase complexed with oxaloacetate

PDB DOI: https://doi.org/10.2210/pdb8KIB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-23 Released: 2024-09-04
Deposition Author(s): Kang, B.S., Cho, H.Y.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203
R-Value Work: 0.175
R-Value Observed: 0.175

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

NADP+-dependent cytosolic isocitrate dehydrogenase complexed with oxaloacetate

Kang, B.S., Cho, H.Y.

To be published.

Macromolecule Content

Total Structure Weight: 190.57 kDa
Atom Count: 14,994
Modelled Residue Count: 1,645
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B, C, D	414	Mus musculus	Mutation(s): 0 Gene Names: Idh1 EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O88844 (Mus musculus) Explore O88844 Go to UniProtKB: O88844
IMPC: MGI:96413
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O88844
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	E [auth A], J [auth B], O [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C]
OAA (Subject of Investigation/LOI) Query on OAA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	F [auth A] G [auth A] K [auth B] L [auth B] P [auth C] F [auth A], G [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], T [auth D]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	H [auth A] I [auth A] M [auth B] N [auth B] R [auth C] H [auth A], I [auth A], M [auth B], N [auth B], R [auth C], S [auth C], U [auth D], V [auth D]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D]