Research workbench
Crystal structure of tRNA (M1A58) methyltransferase trmi from aquifex aeolicus
Analyse Crystal structure of tRNA (M1A58) methyltransferase trmi from aquifex aeolicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YVL
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- EC
- 2.1.1.36
- UniProt
- O66653
- Ligands
- SAM
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hypothetical protein (EC 2.1.1.36) | protein | 247 | 27% helix, 32% strand | O66653 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.74 | 0.99 | 20 | empty |
| 2 | 755 | 0.71 | 0.77 | 82 | SAM |
| 3 | 720 | 0.70 | 0.77 | 75 | SAM |
| 4 | 500 | 0.66 | 0.77 | 44 | empty |
| 5 | 474 | 0.63 | 0.76 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2734 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 2710 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 923 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 879 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 215 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2YVL · Crystal structure of tRNA (m1A58) methyltransferase TrmI from Aquifex aeolicus · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O66653
- Elsewhere: RCSB PDB 2YVL · PDBe 2YVL · UniProt O66653
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