2Y1H

Crystal structure of the human TatD-domain protein 3 (TATDN3)

PDB DOI: https://doi.org/10.2210/pdb2Y1H/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-12-08 Released: 2010-12-29
Deposition Author(s): Muniz, J.R.C., Puranik, S., Krojer, T., Yue, W.W., Ugochukwu, E., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Kavanagh, K.L., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.217
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Human Tatd-Domain Protein 3 (Tatdn3)

Muniz, J.R.C., Puranik, S., Krojer, T., Yue, W.W., Ugochukwu, E., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Kavanagh, K.L., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 60.95 kDa
Atom Count: 3,986
Modelled Residue Count: 527
Deposited Residue Count: 544
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE DEOXYRIBONUCLEASE TATDN3	A, B	272	Homo sapiens	Mutation(s): 0 EC: 3.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q17R31 (Homo sapiens) Explore Q17R31 Go to UniProtKB: Q17R31
PHAROS: Q17R31 GTEx: ENSG00000203705
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q17R31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A]	C [auth A], D [auth A], 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 G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.217
R-Value Work: 0.177
R-Value Observed: 0.179
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.91	α = 90
b = 44.91	β = 90
c = 233.112	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-12-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-29
Type: Initial release
Version 1.1: 2012-12-05
Changes: Database references, Source and taxonomy, Structure summary, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references

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Help and Resources

2Y1H

Crystal structure of the human TatD-domain protein 3 (TATDN3)

Crystal Structure of the Human Tatd-Domain Protein 3 (Tatdn3)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)