4II1 | pdb_00004ii1

Crystal structure of the zinc finger of ZGPAT

PDB DOI: https://doi.org/10.2210/pdb4II1/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-12-19 Released: 2013-02-13
Deposition Author(s): Bian, C., Tempel, W., Dong, A., Chao, X., Fu, M., Wernimont, A.K., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.242 (Depositor), 0.255 (DCC)
R-Value Work:
0.208 (Depositor), 0.229 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4II1

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

Literature

Crystal structure of the zinc finger of ZGPAT

Bian, C., Tempel, W., Dong, A., Chao, X., Fu, M., Wernimont, A.K., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J.

To be published.

Macromolecule Content

Total Structure Weight: 75.37 kDa
Atom Count: 3,977
Modeled Residue Count: 543
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger CCCH-type with G patch domain-containing protein	A, B, C, D	167	Homo sapiens	Mutation(s): 0 Gene Names: ZGPAT, GPATC6, GPATCH6, KIAA1847, ZC3H9, ZC3HDC9, ZIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5A5 (Homo sapiens) Explore Q8N5A5 Go to UniProtKB: Q8N5A5
PHAROS: Q8N5A5 GTEx: ENSG00000197114
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N5A5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], P [auth C], T [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] 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 AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] 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 AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] 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 AA [auth D]	AA [auth D] F [auth A] G [auth A] H [auth A] I [auth A] AA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth D] 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] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] 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] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.242 (Depositor), 0.255 (DCC)
R-Value Work: 0.208 (Depositor), 0.229 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.17	α = 90
b = 87.07	β = 95.65
c = 76.57	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SHELX	phasing
SHARP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Wernimont, A.K.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.