SAXSdb — 3oze

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

;S-methyl-5'-thioadenosine phosphorylase ;

Homo sapiens

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–283 Chain B； UniProt 1–283 Chain C； UniProt 1–283	Not recorded	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；200mM NaCl, 0.1M Hepes, 20% PEG3000, pH 7.5, vapor diffusion, sitting drop, temperature 291K	Resolution 2.00 Å R-free 0.262
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1–283 Chain E； UniProt 1–283 Chain F； UniProt 1–283	Not recorded	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；200mM NaCl, 0.1M Hepes, 20% PEG3000, pH 7.5, vapor diffusion, sitting drop, temperature 291K	Resolution 2.00 Å R-free 0.262

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 3OZE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CB0 STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE AT 1.7 A RESOLUTION Deposited 1999-02-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Mutation：ILE56VAL	ADE ADENINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 1.70 Å R-free 0.202
1CG6 STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE AND SULFATE AT 1.7 A RESOLUTION Deposited 1999-03-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Mutation：ILE56VAL	SO4 SULFATE ION × 3 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；12% (W/V) PEG 6000, 25% (V/V) ETHYLENE GLYCOL, 0.2M TRIS-HCL PH 7.8, 0.002M DTT, pH 7.4	Resolution 1.70 Å R-free 0.225
1K27 Crystal Structure of 5'-Deoxy-5'-Methylthioadenosine Phosphorylase in Complex with a Transition State Analogue Deposited 2001-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	PO4 PHOSPHATE ION × 3 MTM (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 6000, Spermidine, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.207
1SD1 STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH FORMYCIN A Deposited 2004-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；12% (W/V) PEG 6000, 25%(V/V) ETHYLENE GLYCOL, 0.2M Tris-HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.03 Å R-free 0.198
1SD2 STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH 5'-METHYLTHIOTUBERCIDIN Deposited 2004-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	SO4 SULFATE ION × 3 MTH 2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-METHYLSULFANYLMETHYL-TETRAHYDRO-FURAN-3,4-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；12% (W/V) PEG 6000, 25%(V/V) ETHYLENE GLYCOL, 0.2M Tris-HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.207
3LN5 Crystal structure of HLA-B*4104 in complex with a 11mer self-peptide derived from S-methyl-5-thioadenosine phosphorylase Deposited 2010-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 227–237（11 aa） Fragment：UNP residues 227-237	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.1M citrate pH 5.6, 14-20% PEG 4000, 0.2M NH4OAc, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.90 Å R-free 0.241
3OZC Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pCl-phenylthioDADMeImmA Deposited 2010-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	4CT (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol × 3 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；291 K；0.2M NaCl, 0.1M phosphate buffer, 10% PEG 8000, pH 6.2, vapor diffusion, sitting drop, temperature 291K	Resolution 1.93 Å R-free 0.154
3OZD Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pCl-phenylthioDADMeImmA Deposited 2010-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	4CT (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M NaCl, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K	Resolution 2.10 Å R-free 0.257
3OZD Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pCl-phenylthioDADMeImmA Deposited 2010-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 1–283（283 aa）	Not recorded	4CT (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；2M NaCl, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K	Resolution 2.10 Å R-free 0.257
5EUB Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 2-amino-MTA and sulfate Deposited 2015-11-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	SO4 SULFATE ION × 6 5S7 (2~{R},3~{R},4~{S},5~{S})-2-[2,6-bis(azanyl)purin-9-yl]-5-(methylsulfanylmethyl)oxolane-3,4-diol × 3 CL CHLORIDE ION × 3 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；Protein 15 mg/mL, Reservoir 0.2 M magnesium chloride, 20% (w/v) PEG 3350	Resolution 1.81 Å R-free 0.193
5TC5 Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with butylthio-DADMe-Immucillin-A and chloride Deposited 2016-09-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa） Chain B 1–283（283 aa） Chain C 1–283（283 aa）	Not recorded	BIG (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol × 3 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；Protein (15 mg/mL); Reservoir (3 M sodium chloride and 0.1 M sodium acetate (pH 4.5))	Resolution 1.96 Å R-free 0.217
5TC6 Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with propylthio-immucillin-A Deposited 2016-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	7A6 (2S,3S,4R,5S)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-[(propylsulfanyl)methyl]pyrrolidine-3,4-diol × 3 PO4 PHOSPHATE ION × 3 GOL GLYCEROL × 3 NA SODIUM ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；Protein (15 mg/mL); Reservoir (0.17 M sodium acetate, 85 mM Tris:HCl (pH 8.5), 25% (w/v) PEG 4000 and 15% (v/v) glycerol)	Resolution 1.48 Å R-free 0.185
5TC7 Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 5'-methylthiotubercidin at 1.75 angstrom Deposited 2016-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	PO4 PHOSPHATE ION × 9 MTH 2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-METHYLSULFANYLMETHYL-TETRAHYDRO-FURAN-3,4-DIOL × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；Protein (15 mg/mL); Reservoir (0.2 M lithium sulfate, 0.1 M TRIS pH 8.5 and 20% (w/v) PEG 4000)	Resolution 1.75 Å R-free 0.184
5TC8 Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with methylthio-DADMe-Immucillin-A Deposited 2016-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	TDI (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL × 3 PO4 PHOSPHATE ION × 3 MG MAGNESIUM ION × 6 CL CHLORIDE ION × 3 2PE NONAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；Protein (15 mg/mL); Reservoir (0.2 M magnesium chloride, 0.1 M sodium citrate:citric acid (pH 5.5) and 40% (v/v) PEG 400)	Resolution 1.80 Å R-free 0.180
6DYZ Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((prop-2-yn-1-ylthio)methyl)pyrrolidin-3-ol Deposited 2018-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	CL CHLORIDE ION × 6 PO4 PHOSPHATE ION × 3 EDO 1,2-ETHANEDIOL × 9 OS2 (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(prop-2-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；100 mM HEPES, pH 7.0, 10% w/v PEG6000	Resolution 1.62 Å R-free 0.190
6DZ0 Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol Deposited 2018-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa）	Not recorded	PO4 PHOSPHATE ION × 3 EDO 1,2-ETHANEDIOL × 15 OS3 (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；100 mM HEPES, pH 7.0, 10% w/v PEG6000	Resolution 1.62 Å R-free 0.176
6DZ2 Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol Deposited 2018-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa） Chain B 1–283（283 aa） Chain C 1–283（283 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 10 CL CHLORIDE ION × 4 ACY ACETIC ACID × 1 OS5 (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；100 mM sodium acetate trihydrate, pH 4.6, 2.0 M sodium chloride	Resolution 1.99 Å R-free 0.236
6DZ3 Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol Deposited 2018-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–283（283 aa） Chain B 1–283（283 aa） Chain C 1–283（283 aa）	Not recorded	CL CHLORIDE ION × 5 EDO 1,2-ETHANEDIOL × 7 OS6 (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl]sulfanyl}methyl)pyrrolidin-3-ol × 3 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；100 mM sodium acetate trihydrate, pH 4.6, 2.0 M sodium chloride	Resolution 1.91 Å R-free 0.220

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

View Construct and Data Evidence

UniProt name	MTAP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 1–283 Author chain B； PDBConstruct 1–283； UniProt 1–283 Author chain C； PDBConstruct 1–283； UniProt 1–283 Author chain D； PDBConstruct 1–283； UniProt 1–283 Author chain E； PDBConstruct 1–283； UniProt 1–283 Author chain F； PDBConstruct 1–283； UniProt 1–283

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	3oze
Deposition date deposition_date	2010-09-24
Structure title title	Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase
Keywords keywords	;5'-methylthioadenosine, phosphorylase, MTAP, TRANSFERASE ;; TRANSFERASE
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	43.26 Å
Radius of gyration Rg (electron density) rg_electron	43.28 Å
Forward intensity I(0) i0	454898000.00
Molecular weight molecular_weight	175530.0 kDa
Excluded volume excluded_volume	219900 Å³
Envelope volume envelope_volume	291530 Å³
Hydration-shell volume shell_volume	56093 Å³
Envelope diameter envelope_diameter	144.9 Å
Shell Rg shell_rg	48.39 Å
Envelope Rg envelope_rg	42.45 Å
Shape Rg shape_rg	43.27 Å
Total Rg total_rg	43.54 Å
Total atoms total_atoms	12273
Residues n_residues	1584
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	144.4 Å
Rg (real space) rg_real	43.40 Å
Rg uncertainty (real space) rg_real_error	1.42 Å
I(0) (real space) i0_real	4.5490e+08
I(0) uncertainty (real space) i0_real_error	8.3780e+06
Rg (reciprocal space) rg_reciprocal	43.26 Å
I(0) (reciprocal space) i0_reciprocal	454800000.0000
Solution quality estimate total_estimate	0.8684
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.1 Å
Skewness Skewness skewness	0.340
Kurtosis Kurtosis kurtosis	-0.608
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	90050000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.899; Smooth: 0.763

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;S-methyl-5'-thioadenosine phosphorylase ;
Molecular weight formula_weight	31277.1 kDa
EC 编号 ec_number	2.4.2.28
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12542

MASGTTTTAVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIKNVDCVLLARHGRQHTIMPSKVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIVIIDQFIDRTTMRPQSFYDGSHSCARGVCHIPMAEPFCPKTREVLIETAKKLGLRCHSKGTMVTIEGPRFSSRAESFMFRTWGADVINMTTVPEVVLAKEAGICYASIAMATDYDCWKEHEEAVSVDRVLKTLKENANKAKSLLLTTIPQIGSTEWSETLHNLKNMAQFSVLLPRH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	269

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3ozea_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d3ozeb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d3ozec_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d3ozed_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d3ozee_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d3ozef_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (6 domains)

Domain ID domain_id	3ozeA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	3ozeB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	3ozeC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	3ozeD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	3ozeE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	3ozeF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

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8. Citations (1)

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Unit-cell length a length_a	79.517 Å
Unit-cell length b length_b	81.810 Å
Unit-cell length c length_c	130.282 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2185
R_work r_work	0.2161
R_free r_free	0.2624

fit	/app/data/saxs_computation/oz/3oze/3oze.fit
pddf	/app/data/pr_computation/oz/3oze/3oze.pr.out
profile	/app/data/saxs_computation/oz/3oze/3oze.dat

Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase

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

;S-methyl-5'-thioadenosine phosphorylase ;

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