4TVR | pdb_00004tvr

Tandem Tudor and PHD domains of UHRF2

PDB DOI: https://doi.org/10.2210/pdb4TVR/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-06-27 Released: 2015-06-24
Deposition Author(s): Walker, J.R., Dong, A., Zhang, Q., Ong, M., Duan, S., Li, Y., Bountra, C., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.260 (Depositor), 0.270 (DCC)
R-Value Work:
0.229 (Depositor), 0.240 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the Tandem Tudor and PHD domains of UHRF2

Walker, J.R., Dong, A., Zhang, Q., Ong, M., Duan, S., Li, Y., Bountra, C., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 31.56 kDa
Atom Count: 1,806
Modelled Residue Count: 222
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF2	A	280	Homo sapiens	Mutation(s): 1 Gene Names: UHRF2, NIRF, RNF107 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PU4 (Homo sapiens) Explore Q96PU4 Go to UniProtKB: Q96PU4
PHAROS: Q96PU4 GTEx: ENSG00000147854
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96PU4
Sequence Annotations Expand
Reference Sequence LOADING

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 C [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain F [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	UNKNOWN ATOM OR ION X		Interactions 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] Focus chain K [auth A] Interactions & Density 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] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.260 (Depositor), 0.270 (DCC)
R-Value Work: 0.229 (Depositor), 0.240 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.28	α = 90
b = 71.28	β = 90
c = 120.052	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description, Source and taxonomy
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description