4Q3B
PylD cocrystallized with L-Lysine-Ne-D-lysine and NAD+
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| B | 0008652 | biological_process | amino acid biosynthetic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| C | 0008652 | biological_process | amino acid biosynthetic process |
| C | 0016491 | molecular_function | oxidoreductase activity |
| D | 0008652 | biological_process | amino acid biosynthetic process |
| D | 0016491 | molecular_function | oxidoreductase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE NAI A 901 |
| Chain | Residue |
| A | ALA2 |
| A | PRO205 |
| A | CYS206 |
| A | THR209 |
| A | PRO224 |
| A | ILE226 |
| A | GLU245 |
| A | PRO246 |
| A | LEU247 |
| A | MG903 |
| A | 2YF904 |
| A | ASN121 |
| A | HOH1002 |
| A | HOH1004 |
| A | HOH1040 |
| A | HOH1101 |
| A | HOH1120 |
| A | GLY150 |
| A | LYS151 |
| A | VAL152 |
| A | ASP171 |
| A | ALA172 |
| A | ALA203 |
| A | THR204 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 902 |
| Chain | Residue |
| A | GLU202 |
| A | THR204 |
| A | CYS206 |
| A | PRO227 |
| A | HOH1061 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 903 |
| Chain | Residue |
| A | TYR129 |
| A | GLU245 |
| A | LEU247 |
| A | ILE249 |
| A | GLY250 |
| A | NAI901 |
| site_id | AC4 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE 2YF A 904 |
| Chain | Residue |
| A | LEU3 |
| A | LEU4 |
| A | VAL53 |
| A | GLY58 |
| A | ILE59 |
| A | ILE60 |
| A | PHE63 |
| A | ALA103 |
| A | ASP104 |
| A | ASN121 |
| A | PRO246 |
| A | NAI901 |
| A | HOH1010 |
| A | HOH1024 |
| A | HOH1031 |
| A | HOH1051 |
| A | HOH1101 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 905 |
| Chain | Residue |
| A | SER134 |
| A | TYR136 |
| A | ALA139 |
| A | SER141 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 906 |
| Chain | Residue |
| A | SER45 |
| A | GLN72 |
| A | GLY75 |
| A | PHE76 |
| A | ASP164 |
| A | HOH1052 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL A 907 |
| Chain | Residue |
| A | THR5 |
| A | ASP7 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 908 |
| Chain | Residue |
| A | LYS18 |
| A | ALA19 |
| A | ALA22 |
| A | LEU242 |
| A | ALA244 |
| A | HOH1111 |
| A | HOH1116 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 909 |
| Chain | Residue |
| A | LEU38 |
| A | TYR39 |
| A | HOH1062 |
| A | HOH1112 |
| A | HOH1118 |
| B | ARG135 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 910 |
| Chain | Residue |
| A | PHE165 |
| A | ARG166 |
| A | VAL167 |
| A | GLY185 |
| A | ILE187 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL A 911 |
| Chain | Residue |
| A | PHE154 |
| A | HOH1044 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 912 |
| Chain | Residue |
| A | GLU131 |
| A | SER134 |
| A | LYS163 |
| A | PHE165 |
| A | HOH1089 |
| A | HOH1128 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 913 |
| Chain | Residue |
| A | SER21 |
| A | HOH1077 |
| B | LYS47 |
| B | PHE79 |
| B | EDO906 |
| site_id | BC5 |
| Number of Residues | 28 |
| Details | BINDING SITE FOR RESIDUE NAI B 901 |
| Chain | Residue |
| B | LYS151 |
| B | VAL152 |
| B | TYR170 |
| B | ASP171 |
| B | ALA172 |
| B | ASP173 |
| B | ALA203 |
| B | THR204 |
| B | PRO205 |
| B | THR209 |
| B | PRO224 |
| B | ILE226 |
| B | GLU245 |
| B | PRO246 |
| B | LEU247 |
| B | MG903 |
| B | 2YF904 |
| B | HOH1002 |
| B | HOH1050 |
| B | HOH1060 |
| B | HOH1113 |
| B | HOH1119 |
| B | HOH1129 |
| B | HOH1130 |
| B | ALA2 |
| B | ASN121 |
| B | THR125 |
| B | GLY150 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 902 |
| Chain | Residue |
| B | GLU202 |
| B | THR204 |
| B | CYS206 |
| B | PRO227 |
| B | HOH1009 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 903 |
| Chain | Residue |
| B | TYR129 |
| B | GLU245 |
| B | LEU247 |
| B | ILE249 |
| B | GLY250 |
| B | NAI901 |
| site_id | BC8 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE 2YF B 904 |
| Chain | Residue |
| B | LEU3 |
| B | LEU4 |
| B | VAL53 |
| B | GLY58 |
| B | ILE59 |
| B | ILE60 |
| B | PHE63 |
| B | ALA103 |
| B | ASN121 |
| B | PRO246 |
| B | NAI901 |
| B | HOH1006 |
| B | HOH1010 |
| B | HOH1034 |
| B | HOH1052 |
| B | HOH1113 |
| site_id | BC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 905 |
| Chain | Residue |
| B | LYS32 |
| B | LYS36 |
| B | SER43 |
| B | HOH1061 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 906 |
| Chain | Residue |
| A | GLN17 |
| A | GOL913 |
| A | HOH1078 |
| B | ASP82 |
| B | GLU91 |
| B | ASN95 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B 907 |
| Chain | Residue |
| A | ALA192 |
| B | LYS196 |
| B | GLU217 |
| site_id | CC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL B 908 |
| Chain | Residue |
| B | THR41 |
| B | PHE42 |
| B | LEU259 |
| B | HOH1029 |
| B | HOH1036 |
| site_id | CC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 909 |
| Chain | Residue |
| A | GLU158 |
| A | VAL161 |
| A | GLN162 |
| A | ASN183 |
| A | LEU184 |
| B | LYS36 |
| B | THR41 |
| B | PHE42 |
| site_id | CC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL B 910 |
| Chain | Residue |
| B | LEU9 |
| B | ILE10 |
| B | ASN11 |
| B | ILE12 |
| B | ASN62 |
| B | ALA65 |
| B | SER66 |
| B | PEG916 |
| B | HOH1057 |
| site_id | CC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 911 |
| Chain | Residue |
| A | LYS32 |
| A | TYR73 |
| A | HOH1012 |
| B | GLN72 |
| B | ASP77 |
| B | SER78 |
| B | HOH1117 |
| B | HOH1125 |
| site_id | CC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE GOL B 912 |
| Chain | Residue |
| B | LEU38 |
| site_id | CC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 913 |
| Chain | Residue |
| B | ALA19 |
| B | ARG235 |
| B | LEU242 |
| B | ALA244 |
| site_id | CC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PEG B 914 |
| Chain | Residue |
| A | ALA37 |
| A | ARG135 |
| A | LYS163 |
| B | GLN24 |
| B | GLU25 |
| B | GLY28 |
| B | HOH1088 |
| site_id | DC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG B 915 |
| Chain | Residue |
| A | VAL53 |
| A | ASP85 |
| A | MET102 |
| B | ASP85 |
| B | MET102 |
| site_id | DC2 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE PEG B 916 |
| Chain | Residue |
| A | LEU9 |
| A | ASN11 |
| A | ILE12 |
| A | ASN62 |
| A | ALA65 |
| A | SER66 |
| A | ALA69 |
| A | HOH1086 |
| B | ASN13 |
| B | GOL910 |
| B | HOH1019 |
| B | HOH1056 |
| B | HOH1059 |
| site_id | DC3 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE NAI C 901 |
| Chain | Residue |
| B | ALA207 |
| C | ALA2 |
| C | ASN121 |
| C | THR125 |
| C | GLY150 |
| C | LYS151 |
| C | VAL152 |
| C | ASP171 |
| C | ALA172 |
| C | ASP173 |
| C | LEU176 |
| C | ALA203 |
| C | THR204 |
| C | PRO205 |
| C | PRO224 |
| C | ILE226 |
| C | GLU245 |
| C | PRO246 |
| C | LEU247 |
| C | MG903 |
| C | 2YF904 |
| C | EDO905 |
| C | HOH1008 |
| C | HOH1018 |
| site_id | DC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA C 902 |
| Chain | Residue |
| C | GLU202 |
| C | THR204 |
| C | CYS206 |
| C | PRO227 |
| C | ALA229 |
| C | HOH1017 |
| site_id | DC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 903 |
| Chain | Residue |
| C | TYR129 |
| C | GLU245 |
| C | LEU247 |
| C | ILE249 |
| C | GLY250 |
| C | NAI901 |
| site_id | DC6 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE 2YF C 904 |
| Chain | Residue |
| C | LEU3 |
| C | LEU4 |
| C | PRO52 |
| C | VAL53 |
| C | GLY58 |
| C | ILE59 |
| C | ILE60 |
| C | PHE63 |
| C | ALA103 |
| C | LEU247 |
| C | NAI901 |
| C | EDO905 |
| C | HOH1007 |
| C | HOH1009 |
| C | HOH1012 |
| site_id | DC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 905 |
| Chain | Residue |
| C | ASP105 |
| C | GLN122 |
| C | NAI901 |
| C | 2YF904 |
| site_id | DC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO C 906 |
| Chain | Residue |
| D | LYS36 |
| site_id | DC9 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE NAI D 901 |
| Chain | Residue |
| D | ALA2 |
| D | ASN121 |
| D | THR125 |
| D | VAL147 |
| D | GLY150 |
| D | LYS151 |
| D | VAL152 |
| D | TYR170 |
| D | ASP171 |
| D | ALA172 |
| D | LEU176 |
| D | ALA203 |
| D | THR204 |
| D | PRO205 |
| D | CYS206 |
| D | THR209 |
| D | PRO224 |
| D | ILE226 |
| D | GLU245 |
| D | PRO246 |
| D | LEU247 |
| D | MG903 |
| D | 2YF904 |
| D | HOH1004 |
| D | HOH1016 |
| D | HOH1017 |
| D | HOH1025 |
| site_id | EC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA D 902 |
| Chain | Residue |
| D | GLU202 |
| D | THR204 |
| D | CYS206 |
| D | PRO227 |
| D | ALA229 |
| D | HOH1008 |
| site_id | EC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 903 |
| Chain | Residue |
| D | TYR129 |
| D | GLU245 |
| D | LEU247 |
| D | ILE249 |
| D | GLY250 |
| D | NAI901 |
| site_id | EC3 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE 2YF D 904 |
| Chain | Residue |
| D | LEU3 |
| D | LEU4 |
| D | PRO52 |
| D | VAL53 |
| D | GLY58 |
| D | ILE59 |
| D | ILE60 |
| D | PHE63 |
| D | ALA103 |
| D | ASN121 |
| D | NAI901 |
| D | HOH1001 |
| D | HOH1005 |
| D | HOH1020 |
| D | HOH1022 |
| site_id | EC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL D 905 |
| Chain | Residue |
| D | ASP85 |
| D | TYR89 |
| D | MET102 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 16 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"24916332","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4Q39","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 28 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"23720358","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24916332","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4JK3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4Q3D","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
