SAXSdb — 9ohl

▼

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

rRNA N(6)-adenosine-methyltransferase METTL5

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	Multifunctional methyltransferase subunit TRM112-like protein × 1 （Q9UI30） S-ADENOSYLMETHIONINE × 1 N-(4-{[(3aS,4R,6S,6aR)-6-(3-chlorophenyl)-2-propanoyloctahydrocyclopenta[c]pyrrol-4-yl]oxy}phenyl)acetamide × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	METL5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–209； UniProt 1–209

Multifunctional methyltransferase subunit TRM112-like protein

Homo sapiens

UniProt Q9UI30

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	rRNA N(6)-adenosine-methyltransferase METTL5 × 1 （Q9NRN9） S-ADENOSYLMETHIONINE × 1 N-(4-{[(3aS,4R,6S,6aR)-6-(3-chlorophenyl)-2-propanoyloctahydrocyclopenta[c]pyrrol-4-yl]oxy}phenyl)acetamide × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TR112_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–125； UniProt 1–125

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ohl
Deposition date deposition_date	2025-05-05
Structure title title	TRMT112-METTL5 bound to SAM and FWG-33B
Keywords keywords	tRNA methyltransferase 112 homolog, Methyltransferase-like protein 5, stereoselective probe, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9ohl__assembly_1__model_1

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

Download this curve (.dat)

9ohl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ohl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.84 Å
Rg (electron density)	19.80 Å
Total Rg	20.72 Å
Atom count	2652
Residues	326
Excluded volume	47487 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ohl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	rRNA N(6)-adenosine-methyltransferase METTL5
Molecular weight formula_weight	23752.5 kDa
EC 编号 ec_number	2.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	3113

MKKVRLKELESRLQQVDGFEKPKLLLEQYPTRPHIAACMLYTIHNTYDDIENKVVADLGCGCGVLSIGTAMLGAGLCVGFDIDEDALEIFNRNAEEFELTNIDMVQCDVCLLSNRMSKSFDTVIMNPPFGTKNNKGTDMAFLKTALEMARTAVYSLHKSSTREHVQKKAAEWKIKIDIIAELRYDLPASYKFHKKKSVDIEVDLIRFSF

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

Entity 2 Entity 2 polymer

Description description	Multifunctional methyltransferase subunit TRM112-like protein
Molecular weight formula_weight	14215.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MKLLTHNLLSSHVRGVGSRGFPLRLQATEVRICPVEFNPNFVARMIPKVEWSAFLEAADNLRLIQVPKGPVEGYEENEEFLRTMHHLLLEVEVIEGTLQCPESGRMFPISRGIPNMLLSEEETES

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

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	N-(4-{[(3aS,4R,6S,6aR)-6-(3-chlorophenyl)-2-propanoyloctahydrocyclopenta[c]pyrrol-4-yl]oxy}phenyl)acetamide
Molecular weight formula_weight	426.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	452

▶

Unit-cell length a length_a	56.684 Å
Unit-cell length b length_b	70.640 Å
Unit-cell length c length_c	84.553 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.286 Å
Low-resolution limit resolution_low	47.127 Å
R factor r_factor	—
R_work r_work	0.1864
R_free r_free	0.2174

TRMT112-METTL5 bound to SAM and FWG-33B

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

rRNA N(6)-adenosine-methyltransferase METTL5

State in the Current Structure

Other States of the Same Protein in the Database

Multifunctional methyltransferase subunit TRM112-like protein

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

9ohl__assembly_1__model_1

9ohl__assembly_1__model_1 | I(q)

9ohl__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

TRMT112-METTL5 bound to SAM and FWG-33B

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

rRNA N(6)-adenosine-methyltransferase METTL5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Multifunctional methyltransferase subunit TRM112-like protein

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

9ohl__assembly_1__model_1

9ohl__assembly_1__model_1 | I(q)

9ohl__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)