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1d2c

METHYLTRANSFERASE

Method: X-RAY DIFFRACTION Dmax: 89.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (GLYCINE N-METHYLTRANSFERASE)

Rattus norvegicus

UniProt P13255

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–293 Chain B； UniProt 2–293 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；277 K；PEG 3400, pH 5.6, VAPOR DIFFUSION, temperature 4.0K Resolution 2.50 Å R-free 0.233
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 2–293 Chain B； UniProt 2–293 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；277 K；PEG 3400, pH 5.6, VAPOR DIFFUSION, temperature 4.0K Resolution 2.50 Å R-free 0.233

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 1D2C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BHJ CRYSTAL STRUCTURE OF APO-GLYCINE N-METHYLTRANSFERASE (GNMT) Deposited 1998-06-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–292（292 aa）
Chain B 1–292（292 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；pH 6.8
Resolution 2.50 Å R-free 0.318
1D2G CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE FROM RAT LIVER Deposited 1999-10-08 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–293（292 aa） Fragment：WHOLE ENZYME
Chain B 2–293（292 aa） Fragment：WHOLE ENZYME
Mutation：R175K Mutation：R175K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG-4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.266
1D2G CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE FROM RAT LIVER Deposited 1999-10-08 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–293（292 aa） Fragment：WHOLE ENZYME
Chain B 2–293（292 aa） Fragment：WHOLE ENZYME
Mutation：R175K Mutation：R175K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG-4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.266
1D2H CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLHOMOCYSTEINE Deposited 1999-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–293（292 aa） Fragment：WHOLE ENZYME
Chain B 2–293（292 aa） Fragment：WHOLE ENZYME
Chain C 2–293（292 aa） Fragment：WHOLE ENZYME
Chain D 2–293（292 aa） Fragment：WHOLE ENZYME
Mutation：R175K Mutation：R175K Mutation：R175K Mutation：R175K SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG-4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.247
1KIA Crystal structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate Deposited 2001-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–292（292 aa）
Chain B 1–292（292 aa）
Chain C 1–292（292 aa）
Chain D 1–292（292 aa）
Not recorded ACT ACETATE ION × 4 SAM S-ADENOSYLMETHIONINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.286
1NBH Structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate, GNMT:SAM:Ace Deposited 2002-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–292（292 aa）
Chain B 1–292（292 aa）
Chain C 1–292（292 aa）
Chain D 1–292（292 aa）
Not recorded ACT ACETATE ION × 4 SAM S-ADENOSYLMETHIONINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；296 K；PEG 3400, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.80 Å R-free 0.278
1NBI Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM. Deposited 2002-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–292（292 aa）
Chain B 1–292（292 aa）
Chain C 1–292（292 aa）
Chain D 1–292（292 aa）
Mutation：R175K Mutation：R175K Mutation：R175K Mutation：R175K SAM S-ADENOSYLMETHIONINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；296 K；PEG 3400, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 3.00 Å R-free 0.295
1XVA METHYLTRANSFERASE Deposited 1996-07-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–292（292 aa）
Chain B 1–292（292 aa）
Not recorded ACT ACETATE ION × 4 SAM S-ADENOSYLMETHIONINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 2.20 Å R-free 0.262
2IDJ Crystal Structure of Rat Glycine N-Methyltransferase Apoprotein, Monoclinic Form Deposited 2006-09-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–292（292 aa）
Chain B 1–292（292 aa）
Chain C 1–292（292 aa）
Chain D 1–292（292 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；20% PEG 3350, 0.1 M Ca acetate, 0.025 M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.35 Å R-free 0.272
2IDK Crystal Structure of Rat Glycine N-Methyltransferase Complexed With Folate Deposited 2006-09-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–292（292 aa）
Chain B 1–292（292 aa）
Chain C 1–292（292 aa）
Chain D 1–292（292 aa）
Not recorded C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；20% PEG 3350, 0.1 M Ca acetate, 0.025 M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.55 Å R-free 0.298
3THR Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate Deposited 2011-08-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–293（292 aa）
Chain B 2–293（292 aa）
Chain C 2–293（292 aa）
Chain D 2–293（292 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 4 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；20% PEG 3350, 0.2 M Na-fluoride or Ca-acetate, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.00 Å R-free 0.241
3THS Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate pentaglutamate Deposited 2011-08-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–293（292 aa）
Chain B 2–293（292 aa）
Chain C 2–293（292 aa）
Chain D 2–293（292 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) BME BETA-MERCAPTOETHANOL × 1 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；20% PEG 3350, 0.2 M Na-fluoride or Ca-acetate, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.50 Å R-free 0.280

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNMT_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–292； UniProt 2–293 Author chain B； PDBConstruct 1–292； UniProt 2–293

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 1d2c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d2c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d2c
Deposition date deposition_date1999-09-23
Structure title titleMETHYLTRANSFERASE
Keywords keywordsMETHYLTRANSFERASE, TRANSFERASE; TRANSFERASE
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_guinier27.74 Å
Radius of gyration Rg (electron density) rg_electron26.86 Å
Forward intensity I(0) i069755400.00
Molecular weight molecular_weight64836.0 kDa
Excluded volume excluded_volume81027 ų
Envelope volume envelope_volume100280 ų
Hydration-shell volume shell_volume31285 ų
Envelope diameter envelope_diameter93.2 Å
Shell Rg shell_rg33.96 Å
Envelope Rg envelope_rg26.65 Å
Shape Rg shape_rg26.85 Å
Total Rg total_rg27.65 Å
Total atoms total_atoms4570
Residues n_residues584
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 dmax89.5 Å
Rg (real space) rg_real27.71 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real6.9760e+07
I(0) uncertainty (real space) i0_real_error1.0430e+06
Rg (reciprocal space) rg_reciprocal27.72 Å
I(0) (reciprocal space) i0_reciprocal69760000.0000
Solution quality estimate total_estimate0.9004
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.8 Å
Skewness Skewness skewness0.305
Kurtosis Kurtosis kurtosis-0.476
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18200000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d2ca_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.5 — Glycine N-methyltransferase
Domain ID domain_idd1d2cb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.5 — Glycine N-methyltransferase

CATH v4.4 (4 domains)

Domain ID domain_id1d2cA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily10 — Glycine N-methyltransferase, chain A, domain 1
Domain ID domain_id1d2cA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id1d2cB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily10 — Glycine N-methyltransferase, chain A, domain 1
Domain ID domain_id1d2cB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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8. Citations (1)

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9. Files and Curves (10)