4YVI
Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0002939 | biological_process | tRNA N1-guanine methylation |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006400 | biological_process | tRNA modification |
| A | 0008033 | biological_process | tRNA processing |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0032259 | biological_process | methylation |
| A | 0052906 | molecular_function | tRNA (guanine(37)-N1)-methyltransferase activity |
| B | 0002939 | biological_process | tRNA N1-guanine methylation |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006400 | biological_process | tRNA modification |
| B | 0008033 | biological_process | tRNA processing |
| B | 0008168 | molecular_function | methyltransferase activity |
| B | 0016740 | molecular_function | transferase activity |
| B | 0032259 | biological_process | methylation |
| B | 0052906 | molecular_function | tRNA (guanine(37)-N1)-methyltransferase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 21 |
| Details | binding site for residue SFG A 301 |
| Chain | Residue |
| A | TYR86 |
| A | ILE133 |
| A | GLY134 |
| A | TYR136 |
| A | LEU138 |
| A | THR139 |
| A | GLY140 |
| A | GLY141 |
| A | PRO144 |
| B | ASP169 |
| B | SER170 |
| A | LEU87 |
| B | ASP177 |
| C | G37 |
| A | SER88 |
| A | PRO89 |
| A | GLN90 |
| A | GLY113 |
| A | TYR115 |
| A | GLU116 |
| A | SER132 |
| site_id | AC2 |
| Number of Residues | 20 |
| Details | binding site for residue SFG B 301 |
| Chain | Residue |
| A | SER170 |
| A | ASP177 |
| B | TYR86 |
| B | LEU87 |
| B | SER88 |
| B | PRO89 |
| B | GLN90 |
| B | GLY113 |
| B | TYR115 |
| B | GLU116 |
| B | TRP131 |
| B | SER132 |
| B | ILE133 |
| B | GLY134 |
| B | TYR136 |
| B | LEU138 |
| B | THR139 |
| B | GLY140 |
| B | GLY141 |
| B | PRO144 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 14 |
| Details | Binding site: {} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 332 |
| Chain | Residue | Details |
| A | PRO89 | increase nucleophilicity, steric role |
| A | GLU116 | electrostatic stabiliser, hydrogen bond acceptor |
| A | ARG154 | activator, electrostatic stabiliser, hydrogen bond donor |
| A | ASP169 | activator, hydrogen bond acceptor, hydrogen bond donor, increase nucleophilicity, proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 4 |
| Details | M-CSA 332 |
| Chain | Residue | Details |
| B | PRO89 | increase nucleophilicity, steric role |
| B | GLU116 | electrostatic stabiliser, hydrogen bond acceptor |
| B | ARG154 | activator, electrostatic stabiliser, hydrogen bond donor |
| B | ASP169 | activator, hydrogen bond acceptor, hydrogen bond donor, increase nucleophilicity, proton acceptor, proton donor |
