5YFN | pdb_00005yfn

Human isocitrate dehydrogenase 1 bound with isocitrate

PDB DOI: https://doi.org/10.2210/pdb5YFN/pdb

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

Deposited: 2017-09-21 Released: 2017-10-25
Deposition Author(s): Nordlund, P., Chen, D., Jansson, A., Larsson, A.
Funding Organization(s): Nanyang Technological University

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.173 (Depositor), 0.190 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Human isocitrate dehydrogenase 1 bound with isocitrate

Nordlund, P., Chen, D., Jansson, A., Larsson, A.

To be published.

Macromolecule Content

Total Structure Weight: 95.72 kDa
Atom Count: 6,724
Modeled Residue Count: 824
Deposited Residue Count: 842
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	421	Homo sapiens	Mutation(s): 0 Gene Names: IDH1, PICD EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens) Explore O75874 Go to UniProtKB: O75874
PHAROS: O75874 GTEx: ENSG00000138413
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75874
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICT Query on ICT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A]	D [auth A], G [auth A]	ISOCITRIC ACID C₆ H₈ O₇ ODBLHEXUDAPZAU-ZAFYKAAXSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain G [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A]	C [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.173 (Depositor), 0.190 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.56	α = 90
b = 92	β = 109.94
c = 138.835	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Nanyang Technological University	Singapore	M060080004

Revision History (Full details and data files)

Version 1.0: 2017-10-25
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

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Human isocitrate dehydrogenase 1 bound with isocitrate

Human isocitrate dehydrogenase 1 bound with isocitrate

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

5YFN | pdb_00005yfn