SAXSdb — 5cve

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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	N-terminal peptide from Histone H2B × 1 （P02283） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	N-terminal peptide from Histone H2B × 1 （P02283） 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 A； PDBConstruct 21–243； UniProt 1–223 Author chain B； PDBConstruct 21–243； UniProt 1–223

N-terminal peptide from Histone H2B

OrganismNot specified

UniProt P02283

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	N-terminal Xaa-Pro-Lys N-methyltransferase 1 × 1 （Q9BV86） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	N-terminal Xaa-Pro-Lys N-methyltransferase 1 × 1 （Q9BV86） 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	H2B_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–9； UniProt 2–10 Author chain E； PDBConstruct 1–9； UniProt 2–10

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	5cve
Deposition date deposition_date	2015-07-26
Structure title title	Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH
Keywords keywords	N-terminal methyltransferase, TRANSFERASE-PEPTIDE complex; TRANSFERASE/PEPTIDE
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.

5cve__assembly_1__model_1

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

Download this curve (.dat)

5cve__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cve__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.37 Å
Rg (electron density)	17.02 Å
Total Rg	18.17 Å
Atom count	1922
Residues	238
Excluded volume	34186 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cve__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5cve__assembly_2__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	27589.4 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	A,B
Atom count atom_count	4578

MGSSHHHHHHSSGLVPRGSHMTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR

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	N-terminal peptide from Histone H2B
Molecular weight formula_weight	887.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

XPKTSGKAA

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	754

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5cveA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5cveB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	114.836 Å
Unit-cell length b length_b	66.302 Å
Unit-cell length c length_c	68.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	32.118 Å
R factor r_factor	0.1534
R_work r_work	0.1526
R_free r_free	0.1795

Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH

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

N-terminal peptide from Histone H2B

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

5cve__assembly_1__model_1

5cve__assembly_1__model_1 | I(q)

5cve__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH

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

N-terminal peptide from Histone H2B

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

5cve__assembly_1__model_1

5cve__assembly_1__model_1 | I(q)

5cve__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)