4K6M
Crystal Structure of the full-length Japanese encephalitis virus NS5
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003968 | molecular_function | RNA-dependent RNA polymerase activity |
| A | 0004482 | molecular_function | mRNA 5'-cap (guanine-N7-)-methyltransferase activity |
| A | 0004483 | molecular_function | mRNA (nucleoside-2'-O-)-methyltransferase activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0032259 | biological_process | methylation |
| A | 0039694 | biological_process | viral RNA genome replication |
| B | 0003968 | molecular_function | RNA-dependent RNA polymerase activity |
| B | 0004482 | molecular_function | mRNA 5'-cap (guanine-N7-)-methyltransferase activity |
| B | 0004483 | molecular_function | mRNA (nucleoside-2'-O-)-methyltransferase activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0008168 | molecular_function | methyltransferase activity |
| B | 0032259 | biological_process | methylation |
| B | 0039694 | biological_process | viral RNA genome replication |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE SAH A 1001 |
| Chain | Residue |
| A | SER56 |
| A | HIS110 |
| A | VAL130 |
| A | ASP131 |
| A | VAL132 |
| A | PHE133 |
| A | ASP146 |
| A | SO41011 |
| A | HOH1145 |
| A | HOH1209 |
| A | GLY58 |
| A | GLY81 |
| A | CYS82 |
| A | GLY85 |
| A | GLY86 |
| A | TRP87 |
| A | THR104 |
| A | LYS105 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1002 |
| Chain | Residue |
| A | ARG41 |
| A | ARG45 |
| A | HOH1116 |
| A | HOH1192 |
| B | THR38 |
| B | ARG41 |
| B | HOH1219 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1003 |
| Chain | Residue |
| A | ARG28 |
| A | ARG41 |
| A | ARG57 |
| A | ARG213 |
| B | ARG45 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1004 |
| Chain | Residue |
| A | ARG37 |
| A | ARG41 |
| A | ARG44 |
| A | ARG84 |
| A | HOH1142 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1005 |
| Chain | Residue |
| A | ALA31 |
| A | ARG243 |
| A | ARG246 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1006 |
| Chain | Residue |
| A | ARG28 |
| A | SER215 |
| A | ASN216 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1007 |
| Chain | Residue |
| A | ALA410 |
| A | LEU411 |
| A | GLY412 |
| A | HOH1153 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1008 |
| Chain | Residue |
| A | ARG734 |
| A | ARG742 |
| A | SER799 |
| A | TRP800 |
| A | SER801 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1009 |
| Chain | Residue |
| A | ARG474 |
| A | GLY539 |
| A | LYS694 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1010 |
| Chain | Residue |
| A | GLY561 |
| A | ARG564 |
| B | GLN635 |
| B | HIS636 |
| B | LYS643 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1011 |
| Chain | Residue |
| A | GLY109 |
| A | HIS110 |
| A | GLU111 |
| A | SAH1001 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 1012 |
| Chain | Residue |
| A | GLU440 |
| A | HIS444 |
| A | CYS449 |
| A | CYS452 |
| site_id | BC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 1013 |
| Chain | Residue |
| A | HIS717 |
| A | CYS733 |
| A | GLU848 |
| A | CYS852 |
| site_id | BC5 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE SAH B 1001 |
| Chain | Residue |
| B | SER56 |
| B | GLY58 |
| B | GLY81 |
| B | CYS82 |
| B | GLY85 |
| B | GLY86 |
| B | TRP87 |
| B | THR104 |
| B | LYS105 |
| B | HIS110 |
| B | VAL130 |
| B | ASP131 |
| B | VAL132 |
| B | PHE133 |
| B | ASP146 |
| B | ILE147 |
| B | SO41009 |
| B | HOH1125 |
| B | HOH1162 |
| B | HOH1252 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1002 |
| Chain | Residue |
| A | ARG42 |
| A | ARG45 |
| B | ARG28 |
| B | ARG41 |
| B | ARG57 |
| B | ARG213 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1003 |
| Chain | Residue |
| B | HOH1215 |
| B | ARG37 |
| B | ARG41 |
| B | ARG84 |
| site_id | BC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1004 |
| Chain | Residue |
| B | ALA31 |
| B | ARG243 |
| B | ARG246 |
| site_id | BC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1005 |
| Chain | Residue |
| B | ARG28 |
| B | SER215 |
| B | ASN216 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1006 |
| Chain | Residue |
| B | ALA410 |
| B | LEU411 |
| B | GLY412 |
| site_id | CC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1007 |
| Chain | Residue |
| B | ARG734 |
| B | SER799 |
| B | TRP800 |
| B | SER801 |
| site_id | CC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1008 |
| Chain | Residue |
| B | ARG474 |
| B | GLY539 |
| B | LYS694 |
| site_id | CC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1009 |
| Chain | Residue |
| B | GLY109 |
| B | HIS110 |
| B | GLU111 |
| B | SAH1001 |
| site_id | CC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 1010 |
| Chain | Residue |
| B | HIS717 |
| B | CYS733 |
| B | GLU848 |
| B | CYS852 |
| site_id | CC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 1011 |
| Chain | Residue |
| B | GLU440 |
| B | HIS444 |
| B | CYS449 |
| B | CYS452 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | ACT_SITE: For 2'-O-MTase activity => ECO:0000250|UniProtKB:Q6YMS4 |
| Chain | Residue | Details |
| A | LYS61 | |
| A | ASP146 | |
| A | LYS182 | |
| A | GLU218 | |
| B | LYS61 | |
| B | ASP146 | |
| B | LYS182 | |
| B | GLU218 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 18 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00924 |
| Chain | Residue | Details |
| A | SER56 | |
| B | SER56 | |
| B | GLY86 | |
| B | TRP87 | |
| B | THR104 | |
| B | LYS105 | |
| B | ASP131 | |
| B | VAL132 | |
| B | ILE147 | |
| B | TYR220 | |
| A | GLY86 | |
| A | TRP87 | |
| A | THR104 | |
| A | LYS105 | |
| A | ASP131 | |
| A | VAL132 | |
| A | ILE147 | |
| A | TYR220 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 14 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:24293643 |
| Chain | Residue | Details |
| A | GLU440 | |
| B | CYS449 | |
| B | CYS452 | |
| B | HIS717 | |
| B | CYS733 | |
| B | CYS852 | |
| A | HIS444 | |
| A | CYS449 | |
| A | CYS452 | |
| A | HIS717 | |
| A | CYS733 | |
| A | CYS852 | |
| B | GLU440 | |
| B | HIS444 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 14 |
| Details | SITE: mRNA cap binding => ECO:0000255|PROSITE-ProRule:PRU00924 |
| Chain | Residue | Details |
| A | LYS13 | |
| B | PHE24 | |
| B | ARG28 | |
| B | SER150 | |
| B | ARG213 | |
| B | SER215 | |
| A | ASN17 | |
| A | PHE24 | |
| A | ARG28 | |
| A | SER150 | |
| A | ARG213 | |
| A | SER215 | |
| B | LYS13 | |
| B | ASN17 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | SITE: mRNA cap binding; via carbonyl oxygen => ECO:0000255|PROSITE-ProRule:PRU00924 |
| Chain | Residue | Details |
| A | LEU16 | |
| A | MET19 | |
| B | LEU16 | |
| B | MET19 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | SITE: Essential for 2'-O-methyltransferase activity => ECO:0000255|PROSITE-ProRule:PRU00924 |
| Chain | Residue | Details |
| A | LYS61 | |
| A | LYS182 | |
| A | GLU218 | |
| B | LYS61 | |
| B | LYS182 | |
| B | GLU218 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | SITE: Essential for 2'-O-methyltransferase and N-7 methyltransferase activity => ECO:0000255|PROSITE-ProRule:PRU00924 |
| Chain | Residue | Details |
| A | ASP146 | |
| B | ASP146 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P03314 |
| Chain | Residue | Details |
| A | SER56 | |
| B | SER56 |
