6pva

The structure of NTMT1 in complex with compound 11

Method: X-RAY DIFFRACTION D_max: 56.2 Å Quality: GOOD

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

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 B； UniProt 2–223	Not recorded	;AMINO GROUP-()-LYSINE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine ; × 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 1.84 Å R-free 0.232

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 6PVA	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 experimental conditions 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 experimental conditions 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 experimental conditions 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 ligand/ion Different experimental conditions 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
5E1M Crystal structure of NTMT1 in complex with PPKRIA peptide Deposited 2015-09-29	Different ligand/ion Different experimental conditions 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 × 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
5E1M Crystal structure of NTMT1 in complex with PPKRIA peptide Deposited 2015-09-29	Different ligand/ion Different experimental conditions 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 1.75 Å R-free 0.188
5E1O Crystal structure of NTMT1 in complex with RPKRIA peptide Deposited 2015-09-29	Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 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
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 29 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 B； PDBConstruct 20–241； UniProt 2–223

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	6pva
Deposition date deposition_date	2019-07-20
Structure title title	The structure of NTMT1 in complex with compound 11
Keywords keywords	methyltransferase, enzyme, inhibitor complex, TRANSFERASE, transferase-transferase inhibitor complex; transferase/transferase inhibitor
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	17.84 Å
Radius of gyration Rg (electron density) rg_electron	16.42 Å
Forward intensity I(0) i0	12313500.00
Molecular weight molecular_weight	26112.0 kDa
Excluded volume excluded_volume	32638 Å³
Envelope volume envelope_volume	36517 Å³
Hydration-shell volume shell_volume	18055 Å³
Envelope diameter envelope_diameter	54.9 Å
Shell Rg shell_rg	23.18 Å
Envelope Rg envelope_rg	16.74 Å
Shape Rg shape_rg	16.41 Å
Total Rg total_rg	17.48 Å
Total atoms total_atoms	1836
Residues n_residues	227
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	56.2 Å
Rg (real space) rg_real	17.67 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.2310e+07
I(0) uncertainty (real space) i0_real_error	1.4250e+05
Rg (reciprocal space) rg_reciprocal	17.70 Å
I(0) (reciprocal space) i0_reciprocal	12310000.0000
Solution quality estimate total_estimate	0.8059
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.063
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5528000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	N-terminal Xaa-Pro-Lys N-methyltransferase 1
Molecular weight formula_weight	27320.1 kDa
EC 编号 ec_number	2.1.1.244
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	2001

MGSSHHHHHHSSGLVPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;AMINO GROUP-()-LYSINE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine ;
Molecular weight formula_weight	819.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

XGPKKX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

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8. Citations (1)

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Unit-cell length a length_a	73.012 Å
Unit-cell length b length_b	73.012 Å
Unit-cell length c length_c	82.172 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.840 Å
Low-resolution limit resolution_low	29.510 Å
R factor r_factor	0.1990
R_work r_work	0.1958
R_free r_free	0.2318

fit	/app/data/saxs_computation/pv/6pva/6pva.fit
pddf	/app/data/pr_computation/pv/6pva/6pva.pr.out
profile	/app/data/saxs_computation/pv/6pva/6pva.dat

The structure of NTMT1 in complex with compound 11

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

N-terminal Xaa-Pro-Lys N-methyltransferase 1

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)