SAXSdb — 1ndz

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

Adenosine Deaminase

OrganismNot specified

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 1–356	Not recorded	ZN ZINC ION × 1 FR5 1-((1R)-1-(HYDROXYMETHYL)-3-(6-((3-(1-METHYL-1H-BENZIMIDAZOL-2-YL)PROPANOYL)AMINO)-1H-INDOL-1-YL)PROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium phosphate, PEG400, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.225

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 1NDZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KRM Crystal structure of bovine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine riboside Deposited 2002-01-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 PRH 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；ammonium sulphate, PEG400, MES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.198
1NDV Crystal Structure of Adenosine Deaminase complexed with FR117016 Deposited 2002-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FR0 N''-(4-(5-((1H-BENZIMIDAZOL-2-YLAMINO)METHYL)-2-THIENYL)-1,3-THIAZOL-2-YL)GUANIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium sulfate, PEG400, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
1NDW Crystal Structure of Adenosine Deaminase Complexed with FR221647 Deposited 2002-12-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FR2 1-((1R)-1-(HYDROXYMETHYL)-3-PHENYLPROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium phosphate, PEG400, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.218
1NDY Crystal Structure of Adenosine Deaminase Complexed with FR230513 Deposited 2002-12-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FR3 1-((1R)-1-(HYDROXYMETHYL)-3-(1-NAPHTHYL)PROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium phosphate, PEG400, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.210
1O5R Crystal structure of adenosine deaminase complexed with a potent inhibitor Deposited 2003-10-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FR9 1-[(1R)-3-(6-{[(BENZYLAMINO)CARBONYL]AMINO}-1H-INDOL-1-YL)-1-(HYDROXYMETHYL)PROPYL]-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium sulphate, PEG400, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.35 Å R-free 0.242
1QXL Crystal structure of Adenosine deaminase complexed with FR235380 Deposited 2003-09-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FR8 1-((1R)-1-(HYDROXYMETHYL)-3-{6-[(5-PHENYLPENTANOYL)AMINO]-1H-INDOL-1-YL}PROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium phosphate, PEG400, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.25 Å R-free 0.253
1UML Crystal structure of adenosine deaminase complexed with a potent inhibitor FR233624 Deposited 2003-10-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FR4 1-((1R)-1-(HYDROXYMETHYL)-3-{6-[(3-PHENYLPROPANOYL)AMINO]-1H-INDOL-1-YL}PROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium sulphate, PEG400, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.286
1V79 Crystal structures of adenosine deaminase complexed with potent inhibitors Deposited 2003-12-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FR7 1-{(1R,2S)-1-[2-(2,3,-DICHLOROPHENYL)ETHYL]-2-HYDROXYPROPYL}-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium sulphate, PEG400, MES buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.281
1V7A Crystal structures of adenosine deaminase complexed with potent inhibitors Deposited 2003-12-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FRC 1-{(1R,2S)-2-HYDROXY-1-[2-(2-NAPHTHYLOXY)ETHYL]PROPYL}-1H-IMIDAZONE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammoniun sulphate, PEG400, MES buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.276
1VFL Adenosine deaminase Deposited 2004-04-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；PEG4000, 2-propanol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.267
1W1I Crystal structure of dipeptidyl peptidase IV (DPPIV or CD26) in complex with adenosine deaminase Deposited 2004-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 0–356（357 aa） Chain F 0–356（357 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 3.03 Å R-free 0.257
1W1I Crystal structure of dipeptidyl peptidase IV (DPPIV or CD26) in complex with adenosine deaminase Deposited 2004-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 0–356（357 aa） Chain H 0–356（357 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 3.03 Å R-free 0.257
1WXY Crystal structure of adenosine deaminase ligated with a potent inhibitor Deposited 2005-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FRK N-[4,5-BIS(4-HYDROXYPHENYL)-1,3-THIAZOL-2-YL]HEXANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Ammonium sulphate, PEG400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.280
1WXZ Crystal structure of adenosine deaminase ligated with a potent inhibitor Deposited 2005-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FRL 1-((1R,2S)-1-{2-[2-(4-CHLOROPHENYL)-1,3-BENZOXAZOL-7-YL]ETHYL}-2-HYDROXYPROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Ammonium sulphate, PEG400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.223
2BGN HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26) Deposited 2005-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–362（362 aa） Chain F 1–362（362 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.15 Å R-free 0.247
2BGN HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26) Deposited 2005-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–362（362 aa） Chain H 1–362（362 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.15 Å R-free 0.247
2E1W Crystal structure of adenosine deaminase complexed with potent inhibitors Deposited 2006-10-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–356（356 aa）	Not recorded	ZN ZINC ION × 1 FR6 1-{(1R,2S)-2-HYDROXY-1-[2-(1-NAPHTHYL)ETHYL]PROPYL}-1H-IMIDAZOLE-4-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；ammonium sulphate, PEG400, MES buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.246
2Z7G Crystal structure of adenosine deaminase ligated with EHNA Deposited 2007-08-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–357（356 aa）	Not recorded	ZN ZINC ION × 1 EH9 (2S,3R)-3-(6-amino-9H-purin-9-yl)nonan-2-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；2M Ammonium sulfate, 2% MPD, 0.1M MES buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.52 Å R-free 0.247

16 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ADA_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–356； UniProt 1–356

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	1ndz
Deposition date deposition_date	2002-12-09
Structure title title	Crystal Structure of Adenosine Deaminase Complexed with FR235999
Keywords keywords	SBDD, TIM-barrel, hydrolase; HYDROLASE
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	20.09 Å
Radius of gyration Rg (electron density) rg_electron	19.04 Å
Forward intensity I(0) i0	26929500.00
Molecular weight molecular_weight	40125.0 kDa
Excluded volume excluded_volume	50253 Å³
Envelope volume envelope_volume	54997 Å³
Hydration-shell volume shell_volume	23160 Å³
Envelope diameter envelope_diameter	63.8 Å
Shell Rg shell_rg	26.36 Å
Envelope Rg envelope_rg	19.37 Å
Shape Rg shape_rg	19.04 Å
Total Rg total_rg	19.97 Å
Total atoms total_atoms	2826
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	63.9 Å
Rg (real space) rg_real	19.96 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	2.6930e+07
I(0) uncertainty (real space) i0_real_error	3.1630e+05
Rg (reciprocal space) rg_reciprocal	19.98 Å
I(0) (reciprocal space) i0_reciprocal	26930000.0000
Solution quality estimate total_estimate	0.8895
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.448
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9262000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.999

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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	40341.7 kDa
EC 编号 ec_number	3.5.4.4
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3371

AQTPAFDKPKVELHVHLDGAIKPETILYYGKRRGIALPADTPEELQNIIGMDKPLTLPDFLAKFDYYMPAIAGCRDAIKRIAYEFVEMKAKDGVVYVEVRYSPHLLANSKVEPIPWNQAEGDLTPDEVVSLVNQGLQEGERDFGVKVRSILCCMRHQPSWSSEVVELCKKYREQTVVAIDLAGDETIEGSSLFPGHVQAYAEAVKSGVHRTVHAGEVGSANVVKEAVDTLKTERLGHGYHTLEDTTLYNRLRQENMHFEICPWSSYLTGAWKPDTEHAVIRFKNDQVNYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEDEKKELLDLLYKAYRMPSPA

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-((1R)-1-(HYDROXYMETHYL)-3-(6-((3-(1-METHYL-1H-BENZIMIDAZOL-2-YL)PROPANOYL)AMINO)-1H-INDOL-1-YL)PROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE
Molecular weight formula_weight	499.6 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	545

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ndza_
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	1ndzA00
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 (1)

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Unit-cell length a length_a	78.060 Å
Unit-cell length b length_b	78.060 Å
Unit-cell length c length_c	136.710 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2100
R_free r_free	0.2250

fit	/app/data/saxs_computation/nd/1ndz/1ndz.fit
pddf	/app/data/pr_computation/nd/1ndz/1ndz.pr.out
profile	/app/data/saxs_computation/nd/1ndz/1ndz.dat

Crystal Structure of Adenosine Deaminase Complexed with FR235999

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

Adenosine Deaminase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction