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1a4m

ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0

Method: X-RAY DIFFRACTION Dmax: 152.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADENOSINE DEAMINASE

Mus musculus

UniProt P03958

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 4–352 Not recorded ZN ZINC ION × 1 PRH 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0 Resolution 1.95 Å R-free 0.281
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 4–352 Not recorded ZN ZINC ION × 1 PRH 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0 Resolution 1.95 Å R-free 0.281
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 4–352 Not recorded ZN ZINC ION × 1 PRH 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0 Resolution 1.95 Å R-free 0.281
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 4–352 Not recorded ZN ZINC ION × 1 PRH 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0 Resolution 1.95 Å R-free 0.281

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1A4M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A4L ADA STRUCTURE COMPLEXED WITH DEOXYCOFORMYCIN AT PH 7.0 Deposited 1998-01-31 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa）
Not recorded ZN ZINC ION × 1 DCF 2'-DEOXYCOFORMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0
Resolution 2.60 Å R-free 0.272
1A4L ADA STRUCTURE COMPLEXED WITH DEOXYCOFORMYCIN AT PH 7.0 Deposited 1998-01-31 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 4–352（349 aa）
Not recorded ZN ZINC ION × 1 DCF 2'-DEOXYCOFORMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0
Resolution 2.60 Å R-free 0.272
1A4L ADA STRUCTURE COMPLEXED WITH DEOXYCOFORMYCIN AT PH 7.0 Deposited 1998-01-31 Different ligand/ion Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 4–352（349 aa）
Not recorded ZN ZINC ION × 1 DCF 2'-DEOXYCOFORMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0
Resolution 2.60 Å R-free 0.272
1A4L ADA STRUCTURE COMPLEXED WITH DEOXYCOFORMYCIN AT PH 7.0 Deposited 1998-01-31 Different ligand/ion Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 4–352（349 aa）
Not recorded ZN ZINC ION × 1 DCF 2'-DEOXYCOFORMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0
Resolution 2.60 Å R-free 0.272
1ADD A PRE-TRANSITION STATE MIMIC OF AN ENZYME: X-RAY STRUCTURE OF ADENOSINE DEAMINASE WITH BOUND 1-DEAZA-ADENOSINE AND ZINC-ACTIVATED WATER Deposited 1992-12-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa）
Not recorded ZN ZINC ION × 1 1DA 1-DEAZA-ADENOSINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1FKW MURINE ADENOSINE DEAMINASE (D295E) Deposited 1996-02-29 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa）
Mutation：D295E ZN ZINC ION × 1 PUR PURINE RIBOSIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1FKX MURINE ADENOSINE DEAMINASE (D296A) Deposited 1996-02-29 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa）
Mutation：D296A ZN ZINC ION × 1 PRH 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1UIO ADENOSINE DEAMINASE (HIS 238 ALA MUTANT) Deposited 1996-08-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa）
Mutation：H238A ZN ZINC ION × 1 HPR 6-HYDROXY-7,8-DIHYDRO PURINE NUCLEOSIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1UIP ADENOSINE DEAMINASE (HIS 238 GLU MUTANT) Deposited 1996-08-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa）
Mutation：H238E ZN ZINC ION × 1 PUR PURINE RIBOSIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
2ADA ATOMIC STRUCTURE OF ADENOSINE DEAMINASE COMPLEXED WITH A TRANSITION-STATE ANALOG: UNDERSTANDING CATALYSIS AND IMMUNODEFICIENCY MUTATIONS Deposited 1994-12-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–352（352 aa）
Not recorded ZN ZINC ION × 1 HPR 6-HYDROXY-7,8-DIHYDRO PURINE NUCLEOSIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
3KM8 Crystal structuore of adenosine deaminase from mus musculus complexed with 9-deazainosine Deposited 2009-11-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–352（352 aa）
Mutation：E217Q, Y240E 9DI 9-DEAZAINOSINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；10% PEG 2000 MME, 150mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.223
3KM8 Crystal structuore of adenosine deaminase from mus musculus complexed with 9-deazainosine Deposited 2009-11-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–352（352 aa）
Mutation：E217Q, Y240E 9DI 9-DEAZAINOSINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；10% PEG 2000 MME, 150mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.223
3MVI Crystal structure of holo mADA at 1.6 A resolution Deposited 2010-05-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa） Fragment：UNP residues 4-352
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100 mM Tris_HCl, pH 8.5 and 25% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.60 Å R-free 0.205
3MVI Crystal structure of holo mADA at 1.6 A resolution Deposited 2010-05-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 4–352（349 aa） Fragment：UNP residues 4-352
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100 mM Tris_HCl, pH 8.5 and 25% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.60 Å R-free 0.205
3MVT Crystal structure of apo mADA at 2.2A resolution Deposited 2010-05-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa） Fragment：UNP residues 4-352
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；295 K；200 mM Ammonium sulfate, 20 % PEG 3350, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.20 Å R-free 0.245
3MVT Crystal structure of apo mADA at 2.2A resolution Deposited 2010-05-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 4–352（349 aa） Fragment：UNP residues 4-352
Not recorded GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；295 K；200 mM Ammonium sulfate, 20 % PEG 3350, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.20 Å R-free 0.245
3T1G Engineering of organophosphate hydrolase by computational design and directed evolution Deposited 2011-07-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–352（349 aa）
Mutation：D19S,L58Q,F61T,F65W,Q138H,A183I,V218F,D296A,I299E ZN ZINC ION × 4 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1 M Tris-HCl, 0.2 M calcium acetate, 20% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.35 Å R-free 0.250

11 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADA_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–349； UniProt 4–352 Author chain B； PDBConstruct 1–349； UniProt 4–352 Author chain C； PDBConstruct 1–349； UniProt 4–352 Author chain D； PDBConstruct 1–349； UniProt 4–352

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1a4m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a4m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1a4m
Deposition date deposition_date1998-01-31
Structure title titleADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0
Keywords keywordsHYDROLASE, ADENOSINE DEAMINASE, PURINE RIBOSIDE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier45.86 Å
Radius of gyration Rg (electron density) rg_electron45.69 Å
Forward intensity I(0) i0367614000.00
Molecular weight molecular_weight159940.0 kDa
Excluded volume excluded_volume200380 ų
Envelope volume envelope_volume264900 ų
Hydration-shell volume shell_volume47422 ų
Envelope diameter envelope_diameter151.5 Å
Shell Rg shell_rg51.99 Å
Envelope Rg envelope_rg44.20 Å
Shape Rg shape_rg45.69 Å
Total Rg total_rg45.93 Å
Total atoms total_atoms11248
Residues n_residues1396
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax152.3 Å
Rg (real space) rg_real45.92 Å
Rg uncertainty (real space) rg_real_error1.54 Å
I(0) (real space) i0_real3.6760e+08
I(0) uncertainty (real space) i0_real_error6.6160e+06
Rg (reciprocal space) rg_reciprocal45.86 Å
I(0) (reciprocal space) i0_reciprocal367600000.0000
Solution quality estimate total_estimate0.8490
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary67.2 Å
Skewness Skewness skewness0.163
Kurtosis Kurtosis kurtosis-0.773
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25860000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.832
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1a4ma_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.1 — Adenosine/AMP deaminase
Domain ID domain_idd1a4mb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.1 — Adenosine/AMP deaminase
Domain ID domain_idd1a4mc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.1 — Adenosine/AMP deaminase
Domain ID domain_idd1a4md_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.1 — Adenosine/AMP deaminase

CATH v4.4 (4 domains)

Domain ID domain_id1a4mA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily140 — Metal-dependent hydrolases
Domain ID domain_id1a4mB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily140 — Metal-dependent hydrolases
Domain ID domain_id1a4mC00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily140 — Metal-dependent hydrolases
Domain ID domain_id1a4mD00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily140 — Metal-dependent hydrolases
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8. Citations (4)

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9. Files and Curves (10)