5DAB | pdb_00005dab

Crystal structure of FTO-IN115

PDB DOI: https://doi.org/10.2210/pdb5DAB/pdb

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

Deposited: 2015-08-19 Released: 2016-08-24
Deposition Author(s): Chai, J., Zhou, B., Liu, W., Han, Z., Niu, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.241 (Depositor), 0.237 (DCC)
R-Value Work:
0.210 (Depositor), 0.206 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5DAB

Ligand Structure Quality Assessment

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

Literature

Crystal structure of FTO-IN115

Chai, J., Zhou, B., Liu, W., Han, Z., Niu, T.

To be published.

Macromolecule Content

Total Structure Weight: 55.93 kDa
Atom Count: 3,673
Modeled Residue Count: 434
Deposited Residue Count: 479
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent dioxygenase FTO	A	479	Homo sapiens	Mutation(s): 0 Gene Names: FTO, KIAA1752 EC: 1.14.11 (PDB Primary Data), 1.14.11.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0B1 (Homo sapiens) Explore Q9C0B1 Go to UniProtKB: Q9C0B1
PHAROS: Q9C0B1 GTEx: ENSG00000140718
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C0B1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
58W Query on 58W Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	N-(5-chloro-2,4-dihydroxyphenyl)-1-phenylcyclobutanecarboxamide C₁₇ H₁₆ Cl N O₃ BOHOWRMNYYPMPP-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
AKG Query on AKG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
58W	BindingDB: 5DAB	Kd: 1.30e+4 (nM) from 1 assay(s)
58W	BindingDB: 5DAB	IC50: 4950 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.241 (Depositor), 0.237 (DCC)
R-Value Work: 0.210 (Depositor), 0.206 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.681	α = 90
b = 142.681	β = 90
c = 81.998	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	data reduction
PHENIX	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-08-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-24
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.