Download MendeleyCrystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Elkins, P.A., Bonnette, W.G., Stuckey, J.A.To be published.
4YPZ
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
- PDB DOI: https://doi.org/10.2210/pdb4YPZ/pdb
- Classification: transferase/transferase inhibitor
- Organism(s): Haemophilus influenzae Rd KW20
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-03-13 Released: 2016-03-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.194
- R-Value Work: 0.167
- R-Value Observed: 0.169
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| tRNA (guanine-N(1)-)-methyltransferase | 254 | Haemophilus influenzae Rd KW20 | Mutation(s): 0 Gene Names: trmD, HI_0202 EC: 2.1.1.228 |  | |
UniProt | |||||
Find proteins for P43912 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43912 Go to UniProtKB: P43912 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P43912 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 4FL Query on 4FL | B [auth A] | 4-(1H-imidazol-2-yl)pyridine C8 H7 N3 QWZSAEUNIBEKIZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.194
- R-Value Work: 0.167
- R-Value Observed: 0.169
- Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 93.773 | α = 90 |
| b = 93.773 | β = 90 |
| c = 179.162 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| HKL-2000 | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2016-03-16 Deposition Author(s): Elkins, P.A., Bonnette, W.G., Stuckey, J.A.
Revision History (Full details and data files)
- Version 1.0: 2016-03-16
Type: Initial release - Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
