SAXSdb — 1add

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADENOSINE DEAMINASE

Mus musculus

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 1DA 1-DEAZA-ADENOSINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å

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 1ADD	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 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 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 experimental conditions 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 experimental conditions 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 experimental conditions 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
1A4M ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0 Deposited 1998-01-31	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 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
1A4M ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0 Deposited 1998-01-31	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）	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
1A4M ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0 Deposited 1998-01-31	Different ligand/ion Different experimental conditions 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 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
1A4M ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0 Deposited 1998-01-31	Different ligand/ion Different experimental conditions 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 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
1FKW MURINE ADENOSINE DEAMINASE (D295E) Deposited 1996-02-29	Different mutation/modification Different ligand/ion	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 ligand/ion	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	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	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	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 20 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1add
Deposition date deposition_date	1992-12-22
Structure title title	A PRE-TRANSITION STATE MIMIC OF AN ENZYME: X-RAY STRUCTURE OF ADENOSINE DEAMINASE WITH BOUND 1-DEAZA-ADENOSINE AND ZINC-ACTIVATED WATER
Keywords keywords	HYDROLASE(ACTING IN CYCLICAMIDINES); HYDROLASE(ACTING IN CYCLICAMIDINES)
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.97 Å
Radius of gyration Rg (electron density) rg_electron	18.99 Å
Forward intensity I(0) i0	26633300.00
Molecular weight molecular_weight	39981.0 kDa
Excluded volume excluded_volume	50097 Å³
Envelope volume envelope_volume	54392 Å³
Hydration-shell volume shell_volume	22990 Å³
Envelope diameter envelope_diameter	61.5 Å
Shell Rg shell_rg	26.30 Å
Envelope Rg envelope_rg	19.30 Å
Shape Rg shape_rg	18.99 Å
Total Rg total_rg	19.91 Å
Total atoms total_atoms	2812
Residues n_residues	349
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	60.4 Å
Rg (real space) rg_real	19.84 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.6630e+07
I(0) uncertainty (real space) i0_real_error	2.9790e+05
Rg (reciprocal space) rg_reciprocal	19.86 Å
I(0) (reciprocal space) i0_reciprocal	26630000.0000
Solution quality estimate total_estimate	0.9028
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.121
Kurtosis Kurtosis kurtosis	-0.476
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8524000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ADENOSINE DEAMINASE
Molecular weight formula_weight	39715.2 kDa
EC 编号 ec_number	3.5.4.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2922

TPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFLAKFDYYMPVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDLVNQGLQEGEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYEGAVKNGIHRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAWDPKTTHAVVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKELLERLYREYQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1-DEAZA-ADENOSINE
Molecular weight formula_weight	266.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1adda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.1 — Adenosine/AMP deaminase

CATH v4.4 (1 domains)

Domain ID domain_id	1addA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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8. Citations (3)

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Unit-cell length a length_a	102.390 Å
Unit-cell length b length_b	94.280 Å
Unit-cell length c length_c	73.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	127.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1810
R_work r_work	0.1810
R_free r_free	—

fit	/app/data/saxs_computation/ad/1add/1add.fit
pddf	/app/data/pr_computation/ad/1add/1add.pr.out
profile	/app/data/saxs_computation/ad/1add/1add.dat

A PRE-TRANSITION STATE MIMIC OF AN ENZYME: X-RAY STRUCTURE OF ADENOSINE DEAMINASE WITH BOUND 1-DEAZA-ADENOSINE AND ZINC-ACTIVATED WATER