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.

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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 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	F [auth A], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• 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
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other