SAXSdb — 3km8

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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 1–352	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–352	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

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 3KM8	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 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 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 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 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 construct Different mutation/modification 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 construct Different mutation/modification 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 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 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 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 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 construct Different mutation/modification 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 construct Different mutation/modification 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
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 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 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 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 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 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 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 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 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 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 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 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）	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
3MVI Crystal structure of holo mADA at 1.6 A resolution Deposited 2010-05-04	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 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 mutation/modification 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 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） 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 mutation/modification 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 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 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 19 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 1–352； UniProt 1–352 Author chain B； PDBConstruct 1–352； UniProt 1–352

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	3km8
Deposition date deposition_date	2009-11-10
Structure title title	Crystal structuore of adenosine deaminase from mus musculus complexed with 9-deazainosine
Keywords keywords	HYDROLASE, CYCLICAMIDINES, Metal-binding, Nucleotide metabolism; 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	29.86 Å
Radius of gyration Rg (electron density) rg_electron	29.32 Å
Forward intensity I(0) i0	100859000.00
Molecular weight molecular_weight	79860.0 kDa
Excluded volume excluded_volume	100030 Å³
Envelope volume envelope_volume	116900 Å³
Hydration-shell volume shell_volume	33306 Å³
Envelope diameter envelope_diameter	98.6 Å
Shell Rg shell_rg	36.42 Å
Envelope Rg envelope_rg	29.24 Å
Shape Rg shape_rg	29.32 Å
Total Rg total_rg	29.97 Å
Total atoms total_atoms	5616
Residues n_residues	698
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	95.5 Å
Rg (real space) rg_real	29.92 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	1.0090e+08
I(0) uncertainty (real space) i0_real_error	1.5210e+06
Rg (reciprocal space) rg_reciprocal	29.90 Å
I(0) (reciprocal space) i0_reciprocal	100900000.0000
Solution quality estimate total_estimate	0.8904
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.335
Kurtosis Kurtosis kurtosis	-0.634
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	48200000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.936

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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	40010.5 kDa
EC 编号 ec_number	3.5.4.4
Mutation mutation	E217Q, Y240E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5972

MAQTPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFLAKFDYYMPVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDLVNQGLQEGEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYEGAVKNGIHRTVHAGQVGSPEVVREAVDILKTERVGHGEHTIEDEALYNRLLKENMHFEVCPWSSYLTGAWDPKTTHAVVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKELLERLYREYQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	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	9-DEAZAINOSINE
Molecular weight formula_weight	267.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	356

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3km8A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	3km8B00
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	100.337 Å
Unit-cell length b length_b	93.616 Å
Unit-cell length c length_c	85.416 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	37.480 Å
R factor r_factor	0.2031
R_work r_work	0.2020
R_free r_free	0.2231

fit	/app/data/saxs_computation/km/3km8/3km8.fit
pddf	/app/data/pr_computation/km/3km8/3km8.pr.out
profile	/app/data/saxs_computation/km/3km8/3km8.dat

Crystal structuore of adenosine deaminase from mus musculus complexed with 9-deazainosine

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