3IAR | pdb_00003iar

The crystal structure of human adenosine deaminase

• PDB DOI: https://doi.org/10.2210/pdb3IAR/pdb

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


• Deposited: 2009-07-14 Released: 2009-08-11 
• Deposition Author(s): Ugochukwu, E., Zhang, Y., Hapka, E., Yue, W.W., Bray, J.E., Muniz, J., Burgess-Brown, N., Chaikuad, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.185 (Depositor), 0.141 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of human adenosine deaminase

Ugochukwu, E., Zhang, Y., Hapka, E., Yue, W.W., Bray, J.E., Muniz, J., Burgess-Brown, N., Chaikuad, A., Kavanagh, K.L., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 41.91 kDa 
• Atom Count: 3,638 
• Modeled Residue Count: 360 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase	A	367	Homo sapiens	Mutation(s): 0  Gene Names: ADA EC: 3.5.4.4
UniProt & NIH Common Fund Data Resources
Find proteins for P00813 (Homo sapiens) Explore P00813  Go to UniProtKB:  P00813
PHAROS:  P00813 GTEx:  ENSG00000196839

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3D1	B [auth A]	(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol C10 H13 N5 O3 OLXZPDWKRNYJJZ-RRKCRQDMSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3	D [auth A], E [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.185 (Depositor), 0.141 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.07	α = 90
b = 73.51	β = 90
c = 76.66	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Ugochukwu, E., Zhang, Y., Hapka, E., Yue, W.W., Bray, J.E., Muniz, J., Burgess-Brown, N., Chaikuad, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description