4NN2

Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6

PDB DOI: https://doi.org/10.2210/pdb4NN2/pdb

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

Deposited: 2013-11-16 Released: 2014-02-26
Deposition Author(s): Liu, Z., Li, F., Zhang, J., Mei, Y., Wu, J., Shi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.176
R-Value Work: 0.159
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the second extended PHD domain of human PHF6 protein

Liu, Z., Li, F., Zhang, J., Mei, Y., Wu, J., Shi, Y.

(2014) J Biol Chem

Macromolecule Content

Total Structure Weight: 29.37 kDa
Atom Count: 2,174
Modelled Residue Count: 242
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger protein 6	A, B	129	Homo sapiens	Mutation(s): 0 Gene Names: PHF6, KIAA1823
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWS0 (Homo sapiens) Explore Q8IWS0 Go to UniProtKB: Q8IWS0
PHAROS: Q8IWS0 GTEx: ENSG00000156531
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IWS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.176
R-Value Work: 0.159
R-Value Observed: 0.160
Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.78	α = 90
b = 102.78	β = 90
c = 51.25	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-02-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-26
Type: Initial release
Version 1.1: 2014-12-03
Changes: Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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Help and Resources

4NN2

Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6

Crystal Structure of the second extended PHD domain of human PHF6 protein

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)