SAXSdb — 6pvb

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	;AMINO GROUP-()-(2~{S})-2-azanylpropanal-()-ISOLEUCINE-()-ARGININE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-9-(5-{[(3S)-3-amino-3-carboxypropyl](pentyl)amino}-5-deoxy-beta-L-arabinofuranosyl)-9H-purin-6-amine ; × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6pvb
Deposition date deposition_date	2019-07-20
Structure title title	The structure of NTMT1 in complex with compound 6
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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6pvb__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6pvb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6pvb__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	17.86 Å
Rg (electron density)	16.45 Å
Total Rg	17.48 Å
Atom count	1875
Residues	230
Excluded volume	33311 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6pvb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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	2058

MGSSHHHHHHSSGLVPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;AMINO GROUP-()-(2~{S})-2-azanylpropanal-()-ISOLEUCINE-()-ARGININE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-9-(5-{[(3S)-3-amino-3-carboxypropyl](pentyl)amino}-5-deoxy-beta-L-arabinofuranosyl)-9H-purin-6-amine ;
Molecular weight formula_weight	1044.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

XGPKRIAX

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	nat
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	163

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Unit-cell length a length_a	72.947 Å
Unit-cell length b length_b	72.947 Å
Unit-cell length c length_c	82.089 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	1.500 Å
Low-resolution limit resolution_low	29.480 Å
R factor r_factor	0.2057
R_work r_work	0.2048
R_free r_free	0.2243

The structure of NTMT1 in complex with compound 6

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6pvb__assembly_1__model_1

6pvb__assembly_1__model_1 | I(q)

6pvb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

The structure of NTMT1 in complex with compound 6

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6pvb__assembly_1__model_1

6pvb__assembly_1__model_1 | I(q)

6pvb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)