9fim

compound 1 bound KMT9 crystal structure

Method: X-RAY DIFFRACTION D_max: 66.8 Å Quality: REASONABLE

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

Methyltransferase N6AMT1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 13–214	Not recorded	Multifunctional methyltransferase subunit TRM112-like protein × 1 （Q9UI30） 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

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 9FIM	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 construct 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 construct 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 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 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 construct 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
6PED Crystal structure of HEMK2-TRMT112 complex Deposited 2019-06-20	Different construct 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	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
8CNC Structure of compound 1 bound KMT9 Deposited 2023-02-22	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 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 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
9FKE SAH bound KMT9 crystal structure Deposited 2024-06-03	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 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 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 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 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 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 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 2–203； UniProt 13–214

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 2–125	Not recorded	Methyltransferase N6AMT1 × 1 （Q9Y5N5） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9FIM	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 construct 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 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 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 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 1–125（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 construct 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 construct 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 construct 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 construct 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 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 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 construct 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
6PED Crystal structure of HEMK2-TRMT112 complex Deposited 2019-06-20	Different construct 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	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
7WTS Cryo-EM structure of a human pre-40S ribosomal subunit - State UTP14 Deposited 2022-02-05	Different construct 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 construct 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 construct 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 construct 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 construct 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 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 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 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
9FKE SAH bound KMT9 crystal structure Deposited 2024-06-03	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 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 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 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 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 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 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 construct 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 3–126； UniProt 2–125

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9fim
Deposition date deposition_date	2024-05-29
最后修订 last_revision	2025-06-11
Structure title title	compound 1 bound KMT9 crystal structure
Keywords keywords	Protein transferase, gene regulation, 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	20.42 Å
Radius of gyration Rg (electron density) rg_electron	19.50 Å
Forward intensity I(0) i0	39731700.00
Molecular weight molecular_weight	32611.0 kDa
Excluded volume excluded_volume	31544 Å³
Envelope volume envelope_volume	51006 Å³
Hydration-shell volume shell_volume	21606 Å³
Envelope diameter envelope_diameter	68.9 Å
Shell Rg shell_rg	26.29 Å
Envelope Rg envelope_rg	19.83 Å
Shape Rg shape_rg	19.48 Å
Total Rg total_rg	20.21 Å
Total atoms total_atoms	2468
Residues n_residues	316
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	66.8 Å
Rg (real space) rg_real	20.34 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	3.9730e+07
I(0) uncertainty (real space) i0_real_error	5.1730e+05
Rg (reciprocal space) rg_reciprocal	20.36 Å
I(0) (reciprocal space) i0_reciprocal	39730000.0000
Solution quality estimate total_estimate	0.6985
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.275
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9800000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.999; Smooth: 0.984

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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	Methyltransferase N6AMT1
Molecular weight formula_weight	21804.1 kDa
EC 编号 ec_number	2.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2605

SHVGRGAFSDVYEPAEDTFLLLDALEAAAAELAGVEICLEVGSGSGVVSAFLASMIGPQALYMCTDINPEAAACTLETARCNKVHIQPVITDLVKGLLPRLTEKVDLLVFNPPYVVTPPQEVGSHGIEAAWAGGRNGREVMDRFFPLVPDLLSPRGLFYLVTIKENNPEEILKIMKTKGLQGTTALSRQAGQETLSVLKFTKS

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 polymer

Description description	Multifunctional methyltransferase subunit TRM112-like protein
Molecular weight formula_weight	14272.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGKLLTHNLLSSHVRGVGSRGFPLRLQATEVRICPVEFNPNFVARMIPKVEWSAFLEAADNLRLIQVPKGPVEGYEENEEFLRTMHHLLLEVEVIEGTLQCPESGRMFPISRGIPNMLLSEEETES

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 3 Entity 3 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	468.5 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	116

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8. Citations (1)

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Unit-cell length a length_a	110.027 Å
Unit-cell length b length_b	110.027 Å
Unit-cell length c length_c	129.737 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	47.640 Å
R factor r_factor	—
R_work r_work	0.1590
R_free r_free	0.1866

fit	/app/data/saxs_computation/fi/9fim/9fim.fit
pddf	/app/data/pr_computation/fi/9fim/9fim.pr.out
profile	/app/data/saxs_computation/fi/9fim/9fim.dat

compound 1 bound KMT9 crystal structure

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

Methyltransferase N6AMT1

State in the Current Structure

Other States of the Same Protein in the Database

Multifunctional methyltransferase subunit TRM112-like protein

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)