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6dub

Crystal structure of a methyltransferase

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha N-terminal protein methyltransferase 1B

Homo sapiens

UniProt Q5VVY1

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 A； UniProt 58–278 Fragment：UNP residues 58-278 RCC1 × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 2 UNX UNKNOWN LIGAND × 37 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000, 0.1 M potassium thiocyanate Resolution 1.20 Å R-free 0.178
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 58–278 Fragment：UNP residues 58-278 RCC1 × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 23 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000, 0.1 M potassium thiocyanate Resolution 1.20 Å R-free 0.178

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 6DUB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5UBB Crystal structure of human alpha N-terminal protein methyltransferase 1B Deposited 2016-12-20 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 58–278（221 aa） Fragment：UNP residues 58-278
Not recorded SAM S-ADENOSYLMETHIONINE × 2 UNX UNKNOWN LIGAND × 52 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M sodium acetate
Resolution 2.00 Å R-free 0.250
6KDR Crystal structure of human NRMT2 in complex with human centromere protein B peptide Deposited 2019-07-02 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 61–283（223 aa） Fragment：Protein N-terminal methyltransferase
Chain B 61–283（223 aa） Fragment：Protein N-terminal methyltransferase
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；291 K；0.1M Tris pH 8.3, 6% w/v Polyethylene glycol 8000
Resolution 2.11 Å R-free 0.205
6KDS Crystal structure of human NRMT2 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 61–283（223 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.1；291 K；0.1M Tris pH 8.1, 14% w/v Polyethylene glycol 8000
Resolution 1.84 Å R-free 0.205

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NTM1B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–222； UniProt 58–278 Author chain B； PDBConstruct 2–222； UniProt 58–278

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

暂无 SAXS 图

P(r) Distance Distribution P(r) Distribution

暂无 P(r) 图
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dub
Deposition date deposition_date2018-06-20
Structure title titleCrystal structure of a methyltransferase
Keywords keywordsmethyltransferase, Structural Genomics, Structural Genomics Consortium, SGC, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6dubA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id6dubB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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8. Citations (1)

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9. Files and Curves (0)