4DO0

Crystal Structure of human PHF8 in complex with Daminozide

PDB DOI: https://doi.org/10.2210/pdb4DO0/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-09 Released: 2012-03-14
Deposition Author(s): Krojer, T., Daniel, M., Ng, S.S., Walport, L.J., Chowdhury, R., Arrowsmith, C.H., Edwards, A., Bountra, C., Kawamura, A., Muller-Knapp, S., McDonough, M.A., von Delft, F., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.265
R-Value Work: 0.208
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 44.51 kDa
Atom Count: 2,985
Modelled Residue Count: 363
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone lysine demethylase PHF8	A	374	Homo sapiens	Mutation(s): 0 Gene Names: PHF8, KIAA1111, ZNF422
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPP1 (Homo sapiens) Explore Q9UPP1 Go to UniProtKB: Q9UPP1
PHAROS: Q9UPP1 GTEx: ENSG00000172943
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UPP1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DZA Query on DZA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	DAMINOZIDE C₆ H₁₂ N₂ O₃ NOQGZXFMHARMLW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions 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] Interactions & Density 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]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	J [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A]	K [auth A], N [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain N [auth A] Interactions & Density Focus chain K [auth A] Focus chain N [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
DZA	BindingDB: 4DO0	IC50: 550 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.265
R-Value Work: 0.208
R-Value Observed: 0.211
Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.734	α = 90
b = 151.734	β = 90
c = 151.734	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection, Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description