3DH1

Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2

PDB DOI: https://doi.org/10.2210/pdb3DH1/pdb

Deposited: 2008-06-16 Released: 2008-09-09
Deposition Author(s): Welin, M., Tresaugues, L., Andersson, J., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nyman, T., Olesen, K., Persson, C., Sagemark, J., Schueler, H., Thorsell, A.G., van der Berg, S., Wisniewska, M., Wikstrom, M., Nordlund, P., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.256
R-Value Work: 0.202
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2.

Welin, M., Tresaugues, L., Andersson, J., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nyman, T., Olesen, K., Persson, C., Sagemark, J., Schueler, H., Thorsell, A.G., van der Berg, S., Wisniewska, M., Wikstrom, M., Nordlund, P.

To be published.

Macromolecule Content

Total Structure Weight: 85.56 kDa
Atom Count: 5,051
Modelled Residue Count: 643
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA-specific adenosine deaminase 2	A, B, C, D	189	Homo sapiens	Mutation(s): 0 Gene Names: ADAT2, DEADC1 EC: 3.5.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6V5 (Homo sapiens) Explore Q7Z6V5 Go to UniProtKB: Q7Z6V5
PHAROS: Q7Z6V5 GTEx: ENSG00000189007
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z6V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.256
R-Value Work: 0.202
R-Value Observed: 0.205
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.53	α = 90
b = 103.12	β = 97.6
c = 77.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3DH1

Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2

Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2.

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)