SAXSdb — 6wh8

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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 4	4HP-PRO-LYS-ARG-NH2, BM-30 × 2 S-ADENOSYL-L-HOMOCYSTEINE × 2 water × 4	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 A； PDBConstruct 20–241； UniProt 2–223 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	6wh8
Deposition date deposition_date	2020-04-07
Structure title title	The structure of NTMT1 in complex with compound BM-30
Keywords keywords	methyltransferase, enzyme, inhibitor complex, TRANSFERASE, transferase-transferase inhibitor complex; TRANSFERASE
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.

6wh8__assembly_1__model_1

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

Download this curve (.dat)

6wh8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wh8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.68 Å
Rg (electron density)	24.71 Å
Total Rg	25.53 Å
Atom count	7299
Residues	458
Excluded volume	65605 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wh8__assembly_1__model_1`	tetrameric （4）	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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	7883

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	4HP-PRO-LYS-ARG-NH2, BM-30
Molecular weight formula_weight	533.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

XPKRX

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	560

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Unit-cell length a length_a	106.867 Å
Unit-cell length b length_b	106.867 Å
Unit-cell length c length_c	205.431 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	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.729 Å
Low-resolution limit resolution_low	29.550 Å
R factor r_factor	0.1804
R_work r_work	0.1799
R_free r_free	0.1999

The structure of NTMT1 in complex with compound BM-30

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

6wh8__assembly_1__model_1

6wh8__assembly_1__model_1 | I(q)

6wh8__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 BM-30

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

6wh8__assembly_1__model_1

6wh8__assembly_1__model_1 | I(q)

6wh8__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)