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6ped

Crystal structure of HEMK2-TRMT112 complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methyltransferase N6AMT1

Homo sapiens

UniProt Q9Y5N5

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–214 Not recorded Multifunctional methyltransferase subunit TRM112-like protein × 1 （Q9UI30） SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；2 M sodium/potassium phosphate Resolution 2.30 Å R-free 0.242

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 6PED Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6H1D Crystal structure of C21orf127-TRMT112 in complex with SAH Deposited 2018-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 8–214（207 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 1.1-1.3 M sodium citrate
Resolution 1.94 Å R-free 0.237
6H1E Crystal structure of C21orf127-TRMT112 in complex with SAH and H4 peptide Deposited 2018-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 8–214（207 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 1.1-1.3 M Sodium Citrate
Resolution 1.90 Å R-free 0.244
6K0X Structure of N6AMT1-TRMT112 Complex with SAM Deposited 2019-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–214（213 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；0.2M ammonium acetate 0.1M sodium citrate tribasic dihydrate PH 5.6 30% Polyethylene glycol 4000
Resolution 2.20 Å R-free 0.213
6KHS Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ Deposited 2019-07-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–214（214 aa）
Not recorded MEQ N5-METHYLGLUTAMINE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.26 Msodium phosphate monobasic monohydrate 0.14 Mpotassium phosphate dibasic pH 5.6
Resolution 1.90 Å R-free 0.220
6KMR Crystal structure of human N6amt1-Trm112 in complex with SAM (space group P6122) Deposited 2019-08-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–214（214 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1M succinic acid, pH 7.0, 15% PEG 3350
Resolution 2.00 Å R-free 0.192
6KMS Crystal structure of human N6amt1-Trm112 in complex with SAM (space group I422) Deposited 2019-08-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–214（214 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.6M (NH4)2SO4, 0.1M MES, pH 6.5, 10% 1,4-Dioxane
Resolution 3.20 Å R-free 0.269
6KMS Crystal structure of human N6amt1-Trm112 in complex with SAM (space group I422) Deposited 2019-08-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–214（214 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.6M (NH4)2SO4, 0.1M MES, pH 6.5, 10% 1,4-Dioxane
Resolution 3.20 Å R-free 0.269
8CNC Structure of compound 1 bound KMT9 Deposited 2023-02-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded 6D6 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.3 M Na3Citrate, 0.1M Tris ph 8.0
Resolution 1.46 Å R-free 0.183
8QDG compound 1a bound KMT9 crystal structure Deposited 2023-08-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded SDU (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-pyrrolidin-3-yl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.2 M Na3Citrate, 0.1M Tris 7.5
Resolution 1.39 Å R-free 0.179
8QDI compound 1b bound KMT9 crystal structure Deposited 2023-08-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded QII (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[2-[(2~{R})-pyrrolidin-2-yl]ethyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.1 M Na3Citrate, 0.1M HEPES 7.25
Resolution 1.47 Å R-free 0.191
9FIM compound 1 bound KMT9 crystal structure Deposited 2024-05-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded A1IC3 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.1 M Na3Citrate, 0.1M Tris 8.5
Resolution 1.60 Å R-free 0.187
9FKE SAH bound KMT9 crystal structure Deposited 2024-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2 M (NH4)2SO4, 0.1M Bis-Tris 6.0
Resolution 1.60 Å R-free 0.203
9FKG compound 2a bound KMT9 structure Deposited 2024-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded A1IC7 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-3-azanyl-3-phenyl-propyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.2 M Na3Citrate, 0.1M Tris 7.5
Resolution 1.59 Å R-free 0.192
9FKM compound 2b bound KMT9 crystal structure Deposited 2024-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded A1IC5 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-3-azanylhexyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.8 M (NH4)2SO4, 0.1M Bis-Tris 6.75
Resolution 1.50 Å R-free 0.201
9FKV compound 2c bound KMT9 crystal structure Deposited 2024-06-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded A1IC8 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{R})-3-azanylbutyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；52% Tacsimate, PH 7.7
Resolution 1.47 Å R-free 0.190
9FKW compound 3a bound KMT9 crystal structure Deposited 2024-06-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded A1IDY (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-(methylamino)propyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.2 M Na3Citrate, 0.1M Tris 7.5
Resolution 1.39 Å R-free 0.173
9FL4 compound 5b bound KMT9 crystal structure Deposited 2024-06-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded A1IC6 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-(2-phenylethylamino)propyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.3 M Na3Citrate, 0.1M HEPES 7.75
Resolution 1.70 Å R-free 0.182
9FL5 compound 3b bound KMT9 crystal structure Deposited 2024-06-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–214（202 aa）
Not recorded 62X 5'-{[(3S)-3-amino-3-carboxypropyl][3-(dimethylamino)propyl]amino}-5'-deoxyadenosine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.2 M Na3Citrate, 0.1M Tris 7.5
Resolution 1.39 Å R-free 0.179

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

View Construct and Data Evidence
UniProt name N6MT1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–233； UniProt 1–214

Multifunctional methyltransferase subunit TRM112-like protein

Homo sapiens

UniProt Q9UI30

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–125 Not recorded Methyltransferase N6AMT1 × 1 （Q9Y5N5） SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；2 M sodium/potassium phosphate Resolution 2.30 Å R-free 0.242

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 6PED Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6G4W Cryo-EM structure of a late human pre-40S ribosomal subunit - State A Deposited 2018-03-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 31-meric
Chain r 1–125（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6H1D Crystal structure of C21orf127-TRMT112 in complex with SAH Deposited 2018-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 1.1-1.3 M sodium citrate
Resolution 1.94 Å R-free 0.237
6H1E Crystal structure of C21orf127-TRMT112 in complex with SAH and H4 peptide Deposited 2018-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–125（124 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 1.1-1.3 M Sodium Citrate
Resolution 1.90 Å R-free 0.244
6H2U Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 1.6A resolution Deposited 2018-07-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–118（118 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；25% PEG 4,000; 0.2 M ammonium sulfate; 100 mM Na citrate pH 5.6
Resolution 1.60 Å R-free 0.215
6H2V Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 2.5A resolution Deposited 2018-07-16 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–125（125 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；25% PEG 4,000; 0.2 M ammonium sulfate; 100 mM Na citrate pH 5.6
Resolution 2.49 Å R-free 0.249
6H2V Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 2.5A resolution Deposited 2018-07-16 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–125（125 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；25% PEG 4,000; 0.2 M ammonium sulfate; 100 mM Na citrate pH 5.6
Resolution 2.49 Å R-free 0.249
6K0X Structure of N6AMT1-TRMT112 Complex with SAM Deposited 2019-05-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–125（125 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；0.2M ammonium acetate 0.1M sodium citrate tribasic dihydrate PH 5.6 30% Polyethylene glycol 4000
Resolution 2.20 Å R-free 0.213
6KHS Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ Deposited 2019-07-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–125（125 aa）
Not recorded MEQ N5-METHYLGLUTAMINE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.26 Msodium phosphate monobasic monohydrate 0.14 Mpotassium phosphate dibasic pH 5.6
Resolution 1.90 Å R-free 0.220
6KMR Crystal structure of human N6amt1-Trm112 in complex with SAM (space group P6122) Deposited 2019-08-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–125（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1M succinic acid, pH 7.0, 15% PEG 3350
Resolution 2.00 Å R-free 0.192
6KMS Crystal structure of human N6amt1-Trm112 in complex with SAM (space group I422) Deposited 2019-08-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–125（125 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.6M (NH4)2SO4, 0.1M MES, pH 6.5, 10% 1,4-Dioxane
Resolution 3.20 Å R-free 0.269
6KMS Crystal structure of human N6amt1-Trm112 in complex with SAM (space group I422) Deposited 2019-08-01 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–125（125 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.6M (NH4)2SO4, 0.1M MES, pH 6.5, 10% 1,4-Dioxane
Resolution 3.20 Å R-free 0.269
7WTS Cryo-EM structure of a human pre-40S ribosomal subunit - State UTP14 Deposited 2022-02-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 22 PDB declaration: 23-meric
Chain r 1–125（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7WTT Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1) Deposited 2022-02-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric
Chain r 1–125（125 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7WTU Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (without CK1) Deposited 2022-02-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 33-meric
Chain r 1–125（125 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7WTV Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A2 Deposited 2022-02-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain r 1–125（125 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7WTW Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A3 Deposited 2022-02-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain r 1–125（125 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8CNC Structure of compound 1 bound KMT9 Deposited 2023-02-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded 6D6 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.3 M Na3Citrate, 0.1M Tris ph 8.0
Resolution 1.46 Å R-free 0.183
8QDG compound 1a bound KMT9 crystal structure Deposited 2023-08-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded SDU (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-pyrrolidin-3-yl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.2 M Na3Citrate, 0.1M Tris 7.5
Resolution 1.39 Å R-free 0.179
8QDI compound 1b bound KMT9 crystal structure Deposited 2023-08-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded QII (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[2-[(2~{R})-pyrrolidin-2-yl]ethyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.1 M Na3Citrate, 0.1M HEPES 7.25
Resolution 1.47 Å R-free 0.191
9FIM compound 1 bound KMT9 crystal structure Deposited 2024-05-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded A1IC3 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.1 M Na3Citrate, 0.1M Tris 8.5
Resolution 1.60 Å R-free 0.187
9FKE SAH bound KMT9 crystal structure Deposited 2024-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2 M (NH4)2SO4, 0.1M Bis-Tris 6.0
Resolution 1.60 Å R-free 0.203
9FKG compound 2a bound KMT9 structure Deposited 2024-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded A1IC7 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-3-azanyl-3-phenyl-propyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.2 M Na3Citrate, 0.1M Tris 7.5
Resolution 1.59 Å R-free 0.192
9FKM compound 2b bound KMT9 crystal structure Deposited 2024-06-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded A1IC5 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-3-azanylhexyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.8 M (NH4)2SO4, 0.1M Bis-Tris 6.75
Resolution 1.50 Å R-free 0.201
9FKV compound 2c bound KMT9 crystal structure Deposited 2024-06-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded A1IC8 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{R})-3-azanylbutyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；52% Tacsimate, PH 7.7
Resolution 1.47 Å R-free 0.190
9FKW compound 3a bound KMT9 crystal structure Deposited 2024-06-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded A1IDY (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-(methylamino)propyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.2 M Na3Citrate, 0.1M Tris 7.5
Resolution 1.39 Å R-free 0.173
9FL4 compound 5b bound KMT9 crystal structure Deposited 2024-06-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded A1IC6 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-(2-phenylethylamino)propyl]amino]-2-azanyl-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.3 M Na3Citrate, 0.1M HEPES 7.75
Resolution 1.70 Å R-free 0.182
9FL5 compound 3b bound KMT9 crystal structure Deposited 2024-06-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–125（124 aa）
Not recorded 62X 5'-{[(3S)-3-amino-3-carboxypropyl][3-(dimethylamino)propyl]amino}-5'-deoxyadenosine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.2 M Na3Citrate, 0.1M Tris 7.5
Resolution 1.39 Å R-free 0.179
9OHL TRMT112-METTL5 bound to SAM and FWG-33B Deposited 2025-05-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–125（125 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 A1CBE N-(4-{[(3aS,4R,6S,6aR)-6-(3-chlorophenyl)-2-propanoyloctahydrocyclopenta[c]pyrrol-4-yl]oxy}phenyl)acetamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；21% PEG3350, 0.36 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5
Resolution 1.29 Å R-free 0.217

26 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TR112_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 19–143； UniProt 1–125

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

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P(r) Distance Distribution P(r) Distribution

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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ped
Deposition date deposition_date2019-06-20
Structure title titleCrystal structure of HEMK2-TRMT112 complex
Keywords keywordsmethyltransferase, complex, Structural Genomics, Structural Genomics Consortium, SGC, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

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

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (0)