[English] 日本語
Yorodumi
- PDB-2ada: ATOMIC STRUCTURE OF ADENOSINE DEAMINASE COMPLEXED WITH A TRANSITI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ada
TitleATOMIC STRUCTURE OF ADENOSINE DEAMINASE COMPLEXED WITH A TRANSITION-STATE ANALOG: UNDERSTANDING CATALYSIS AND IMMUNODEFICIENCY MUTATIONS
ComponentsADENOSINE DEAMINASE
KeywordsHYDROLASE / AMINO / ZINC COFACTOR / BETA/ALPHA BARREL / TRANSITION-STATE INHIBITOR
Function / homology
Function and homology information


mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of mucus secretion / penile erection / positive regulation of germinal center formation / 2'-deoxyadenosine deaminase activity / negative regulation of adenosine receptor signaling pathway ...mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of mucus secretion / penile erection / positive regulation of germinal center formation / 2'-deoxyadenosine deaminase activity / negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / hypoxanthine biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inhibition of non-skeletal tissue mineralization / inosine biosynthetic process / adenosine deaminase / amide catabolic process / adenosine deaminase activity / AMP catabolic process / adenosine catabolic process / germinal center B cell differentiation / positive regulation of T cell differentiation in thymus / dATP catabolic process / negative regulation of leukocyte migration / mucus secretion / positive regulation of smooth muscle contraction / regulation of cell-cell adhesion mediated by integrin / response to purine-containing compound / GMP salvage / allantoin metabolic process / embryonic digestive tract development / trophectodermal cell differentiation / IMP salvage / Peyer's patch development / negative regulation of mature B cell apoptotic process / AMP salvage / negative regulation of thymocyte apoptotic process / germinal center formation / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / anchoring junction / regulation of T cell differentiation / positive regulation of T cell differentiation / leukocyte migration / lung alveolus development / thymocyte apoptotic process / positive regulation of T cell receptor signaling pathway / B cell proliferation / smooth muscle contraction / T cell differentiation / positive regulation of heart rate / positive regulation of B cell proliferation / positive regulation of calcium-mediated signaling / lung development / T cell activation / placenta development / calcium-mediated signaling / liver development / positive regulation of T cell activation / negative regulation of inflammatory response / T cell differentiation in thymus / T cell receptor signaling pathway / in utero embryonic development / response to hypoxia / lysosome / cell adhesion / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Adenosine deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-HYDROXY-7,8-DIHYDRO PURINE NUCLEOSIDE / Adenosine deaminase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsWilson, D.K. / Quiocho, F.A.
Citation
Journal: Science / Year: 1991
Title: Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations.
Authors: Wilson, D.K. / Rudolph, F.B. / Quiocho, F.A.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Crystallographic Observation of a Trapped Tetrahedral Intermediate in a Metalloenzyme
Authors: Wilson, D.K. / Quiocho, F.A.
#2: Journal: Biochemistry / Year: 1993
Title: A Pre-Transition-State Mimic of an Enzyme: X-Ray Structure of Adenosine Deaminase with Bound 1-Deazaadenosine
Authors: Wilson, D.K. / Quiocho, F.A.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Refined 2.5 Angstroms Structure of the Murine Adenosine Deaminase at Ph 6.0
Authors: Sharff, A.J. / Wilson, D.K. / Chang, Z.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Preliminary X-Ray Analysis of Crystals of Murine Adenosine Deaminase
Authors: Wilson, D.K. / Rudolph, F.B. / Harrison, M.L. / Kellems, R.E. / Quiocho, F.A.
History
DepositionDec 2, 1994Processing site: BNL
SupersessionMar 31, 1995ID: 1ADA
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3813
Polymers40,0461
Non-polymers3362
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.360, 94.110, 72.930
Angle α, β, γ (deg.)90.00, 127.19, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein ADENOSINE DEAMINASE


Mass: 40045.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P03958, adenosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HPR / 6-HYDROXY-7,8-DIHYDRO PURINE NUCLEOSIDE


Mass: 270.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPND LIGAND IS FORMED IN ENZYME ACTIVE SITE FROM PURINE RIBOSIDE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal grow
*PLUS
pH: 4.2 / Method: vapor diffusion / Details: Wilson, D.K., (1988) J.Mol.Biol., 200, 613.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
250 mM1dropKCl
350 mMsodium citrate1drop
47.5 %PEG60001drop
515 %PEG60001reservoir

-
Data collection

ReflectionNum. obs: 20445 / % possible obs: 93 % / Observed criterion σ(F): 3
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 72059 / Rmerge(I) obs: 0.0324

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→10 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.195 -
obs0.195 20445
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 20 58 2870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.003
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.366
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more