3KM8 | pdb_00003km8

Crystal structuore of adenosine deaminase from mus musculus complexed with 9-deazainosine

PDB DOI: https://doi.org/10.2210/pdb3KM8/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-11-10 Released: 2010-10-20
Deposition Author(s): Fan, X., Gao, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.223 (Depositor), 0.216 (DCC)
R-Value Work:
0.202 (Depositor), 0.204 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

The Catalytic Mechanism of Adenosine Deaminase from Mouse: An Experimental and Theoretical Study

Wu, X., Fan, X., Gao, Y., Su, X., Zhang, H., Wu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 80.69 kDa
Atom Count: 5,972
Modeled Residue Count: 698
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase	A, B	352	Mus musculus	Mutation(s): 2 Gene Names: Ada EC: 3.5.4.4
UniProt
Find proteins for P03958 (Mus musculus) Explore P03958 Go to UniProtKB: P03958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03958
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9DI Query on 9DI Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	9-DEAZAINOSINE C₁₁ H₁₃ N₃ O₅ WKDMPDYUJKSXBW-KBHCAIDQSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.223 (Depositor), 0.216 (DCC)
R-Value Work: 0.202 (Depositor), 0.204 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.337	α = 90
b = 93.616	β = 97.35
c = 85.416	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
SOLVE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description

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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.