Download MendeleyCrystal structure of HEMK2/TRMT112 in complex with SAH and MEQ
Liao, S., Guo, Q., Zhu, Z.To be published.
6KHS
Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ
- PDB DOI: https://doi.org/10.2210/pdb6KHS/pdb
- Classification: STRUCTURAL PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): No
- Deposited: 2019-07-16 Released: 2020-07-15
- Funding Organization(s): National Natural Science Foundation of China
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.220
- R-Value Work: 0.187
- R-Value Observed: 0.189
Starting Models: experimental
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This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Methyltransferase N6AMT1 | 214 | Homo sapiens | Mutation(s): 0 Gene Names: HEMK2 EC: 2.1.1 (PDB Primary Data), 2.1.1.72 (PDB Primary Data) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9Y5N5 (Homo sapiens) Explore Q9Y5N5 Go to UniProtKB: Q9Y5N5 | |||||
PHAROS: Q9Y5N5 GTEx: ENSG00000156239 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y5N5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Multifunctional methyltransferase subunit TRM112-like protein | 125 | Homo sapiens | Mutation(s): 0 Gene Names: TRMT112 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UI30 (Homo sapiens) Explore Q9UI30 Go to UniProtKB: Q9UI30 | |||||
PHAROS: Q9UI30 GTEx: ENSG00000173113 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UI30 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAH Query on SAH | D [auth A] | S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N |  | ||
| MEQ (Subject of Investigation/LOI) Query on MEQ | C [auth A] | N5-METHYLGLUTAMINE C6 H12 N2 O3 ONXPDKGXOOORHB-BYPYZUCNSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.220
- R-Value Work: 0.187
- R-Value Observed: 0.189
- Space Group: P 61 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 110.218 | α = 90 |
| b = 110.218 | β = 90 |
| c = 130.747 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China | China | 31500601 |
| National Natural Science Foundation of China | China | 31501093 |
Revision History (Full details and data files)
- Version 1.0: 2020-07-15
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
