N-terminal Xaa-Pro-Lys N-methyltransferase 1
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 2–223 | Not recorded | RCC1 × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 2 UNX UNKNOWN LIGAND × 23 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate | Resolution 1.75 Å R-free 0.188 |
| 2 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain B； UniProt 2–223 | Not recorded | RCC1 × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 20 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate | Resolution 1.75 Å R-free 0.188 |
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 5E1M | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2EX4 Crystal Structure of Human methyltransferase AD-003 in complex with S-adenosyl-L-homocysteine Deposited 2005-11-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–224（223 aa）
Chain B
2–224（223 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9.5；300 K；Purified AD-003 was was complexed with S-adenosyl-L-homocysteine (SAH) (Sigma) at 1:5 molar ratio of protein:SAH and crystallized using the hanging drop vapor diffusion method at 20 C by mixing 1.5 l of the protein solution with 1.5 l of the reservoir solution containing 18% PEG 3350, 0.2 M KCl, 0.1 M glycine, pH 9.5., VAPOR DIFFUSION, HANGING DROP, temperature 300K
|
Resolution 1.75 Å R-free 0.258 |
| 5CVD Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide Deposited 2015-07-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–223（223 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 28%(w/v) PEG 4000
|
Resolution 1.30 Å R-free 0.160 |
| 5CVD Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide Deposited 2015-07-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–223（223 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 28%(w/v) PEG 4000
|
Resolution 1.30 Å R-free 0.160 |
| 5CVE Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH Deposited 2015-07-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–223（223 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；291 K；0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 24%(w/v) PEG 4000
|
Resolution 1.50 Å R-free 0.179 |
| 5CVE Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH Deposited 2015-07-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–223（223 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.7；291 K；0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 24%(w/v) PEG 4000
|
Resolution 1.50 Å R-free 0.179 |
| 5E1B Crystal structure of NRMT1 in complex with SPKRIA peptide Deposited 2015-09-29 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 3 UNX UNKNOWN LIGAND × 25 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 1.65 Å R-free 0.176 |
| 5E1B Crystal structure of NRMT1 in complex with SPKRIA peptide Deposited 2015-09-29 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 29 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 1.65 Å R-free 0.176 |
| 5E1D NTMT1 in complex with YPKRIA peptide Deposited 2015-09-29 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 3 UNX UNKNOWN LIGAND × 37 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 1.45 Å R-free 0.169 |
| 5E1D NTMT1 in complex with YPKRIA peptide Deposited 2015-09-29 | Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 20 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 1.45 Å R-free 0.169 |
| 5E1O Crystal structure of NTMT1 in complex with RPKRIA peptide Deposited 2015-09-29 | Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 20 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 2.00 Å R-free 0.189 |
| 5E1O Crystal structure of NTMT1 in complex with RPKRIA peptide Deposited 2015-09-29 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 2.00 Å R-free 0.189 |
| 5E2A Crystal structure of NTMT1 in complex with N-terminally methylated SPKRIA peptide Deposited 2015-09-30 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 3 UNX UNKNOWN LIGAND × 22 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 1.75 Å R-free 0.184 |
| 5E2A Crystal structure of NTMT1 in complex with N-terminally methylated SPKRIA peptide Deposited 2015-09-30 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 1.75 Å R-free 0.184 |
| 5E2B Crystal structure of NTMT1 in complex with N-terminally methylated PPKRIA peptide Deposited 2015-09-30 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 2 UNX UNKNOWN LIGAND × 27 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 1.95 Å R-free 0.188 |
| 5E2B Crystal structure of NTMT1 in complex with N-terminally methylated PPKRIA peptide Deposited 2015-09-30 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 23 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；26% PEG3350, 16% tacsimate
|
Resolution 1.95 Å R-free 0.188 |
| 6DTN The structure of NTMT1 in complex with compound DC100-1 Deposited 2018-06-18 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M lithium sulfate; 0.1 M sodium HEPES 7.5
|
Resolution 1.48 Å R-free 0.189 |
| 6KDQ Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A peptide Deposited 2019-07-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–223（223 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；291 K；0.2M Ammonium acetate, 0.1M Sodium citrate dehydrate pH 5.7, 31% w/v PEG 4000
|
Resolution 1.50 Å R-free 0.180 |
| 6KDQ Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A peptide Deposited 2019-07-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–223（223 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；291 K；0.2M Ammonium acetate, 0.1M Sodium citrate dehydrate pH 5.7, 31% w/v PEG 4000
|
Resolution 1.50 Å R-free 0.180 |
| 6PVA The structure of NTMT1 in complex with compound 11 Deposited 2019-07-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M lithium sulfate; 0.1 M sodium HEPES 7.5
|
Resolution 1.84 Å R-free 0.232 |
| 6PVB The structure of NTMT1 in complex with compound 6 Deposited 2019-07-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M lithium sulfate, 0.1 M sodium HEPES 7.5
|
Resolution 1.50 Å R-free 0.224 |
| 6WH8 The structure of NTMT1 in complex with compound BM-30 Deposited 2020-04-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
2–223（222 aa）
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Na-HEPES, pH 7.5, 1.6 M ammonium sulfate, and 2% PEG 1000
|
Resolution 1.73 Å R-free 0.200 |
| 6WJ7 The structure of NTMT1 in complex with compound C2A Deposited 2020-04-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–223（222 aa）
|
Not recorded | AN6 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.8 M Lithium Chloride 0.1 M Tris: HCl, pH 8.5 32 % (w/v) PEG 4000
|
Resolution 1.42 Å R-free 0.188 |
| 7K3D The structure of NTMT1 in complex with compound DC1-13 Deposited 2020-09-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 VWP N~2~-{(2S)-1-[(naphthalen-1-yl)acetyl]-2,5-dihydro-1H-pyrrole-2-carbonyl}-L-lysyl-L-argininamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.5 M Ammonium sulfate; 0.1 M MES pH 6.5
|
Resolution 2.34 Å R-free 0.259 |
| 7K3D The structure of NTMT1 in complex with compound DC1-13 Deposited 2020-09-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 VWP N~2~-{(2S)-1-[(naphthalen-1-yl)acetyl]-2,5-dihydro-1H-pyrrole-2-carbonyl}-L-lysyl-L-argininamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.5 M Ammonium sulfate; 0.1 M MES pH 6.5
|
Resolution 2.34 Å R-free 0.259 |
| 7SS1 The structure of NTMT1 in complex with compound GD433 Deposited 2021-11-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 AKF (1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluoro-3-hydroxyphenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M CHES: NaOH (pH 9.5), 10% (w/v) PEG 3000
|
Resolution 2.40 Å R-free 0.299 |
| 7SS1 The structure of NTMT1 in complex with compound GD433 Deposited 2021-11-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 AKF (1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluoro-3-hydroxyphenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M CHES: NaOH (pH 9.5), 10% (w/v) PEG 3000
|
Resolution 2.40 Å R-free 0.299 |
| 7U1M Crystal structure of NTMT1 in complex with compound YD206 Deposited 2022-02-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 KYF (1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluorophenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES:NaOH, pH 9.5
10% (w/v) PEG 3000
|
Resolution 3.17 Å R-free 0.283 |
| 7U1M Crystal structure of NTMT1 in complex with compound YD206 Deposited 2022-02-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–223（222 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 KYF (1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluorophenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES:NaOH, pH 9.5
10% (w/v) PEG 3000
|
Resolution 3.17 Å R-free 0.283 |
17 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | NTM1A_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 20–241； UniProt 2–223 Author chain B； PDBConstruct 20–241； UniProt 2–223 |