5TEN
Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,5 Furan Dicarboxylic and NADH with Intact Polyhistidine Tag
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
| A | 0019877 | biological_process | diaminopimelate biosynthetic process |
| A | 0050661 | molecular_function | NADP binding |
| A | 0051287 | molecular_function | NAD binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
| B | 0009085 | biological_process | lysine biosynthetic process |
| B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
| B | 0019877 | biological_process | diaminopimelate biosynthetic process |
| B | 0050661 | molecular_function | NADP binding |
| B | 0051287 | molecular_function | NAD binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
| C | 0009085 | biological_process | lysine biosynthetic process |
| C | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
| C | 0019877 | biological_process | diaminopimelate biosynthetic process |
| C | 0050661 | molecular_function | NADP binding |
| C | 0051287 | molecular_function | NAD binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
| D | 0009085 | biological_process | lysine biosynthetic process |
| D | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
| D | 0019877 | biological_process | diaminopimelate biosynthetic process |
| D | 0050661 | molecular_function | NADP binding |
| D | 0051287 | molecular_function | NAD binding |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0005829 | cellular_component | cytosol |
| E | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
| E | 0009085 | biological_process | lysine biosynthetic process |
| E | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| E | 0016491 | molecular_function | oxidoreductase activity |
| E | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
| E | 0019877 | biological_process | diaminopimelate biosynthetic process |
| E | 0050661 | molecular_function | NADP binding |
| E | 0051287 | molecular_function | NAD binding |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0005829 | cellular_component | cytosol |
| F | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
| F | 0009085 | biological_process | lysine biosynthetic process |
| F | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
| F | 0019877 | biological_process | diaminopimelate biosynthetic process |
| F | 0050661 | molecular_function | NADP binding |
| F | 0051287 | molecular_function | NAD binding |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0005829 | cellular_component | cytosol |
| G | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
| G | 0009085 | biological_process | lysine biosynthetic process |
| G | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| G | 0016491 | molecular_function | oxidoreductase activity |
| G | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
| G | 0019877 | biological_process | diaminopimelate biosynthetic process |
| G | 0050661 | molecular_function | NADP binding |
| G | 0051287 | molecular_function | NAD binding |
| H | 0005737 | cellular_component | cytoplasm |
| H | 0005829 | cellular_component | cytosol |
| H | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
| H | 0009085 | biological_process | lysine biosynthetic process |
| H | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| H | 0016491 | molecular_function | oxidoreductase activity |
| H | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
| H | 0019877 | biological_process | diaminopimelate biosynthetic process |
| H | 0050661 | molecular_function | NADP binding |
| H | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | binding site for residue NAD A 1001 |
| Chain | Residue |
| A | GLY8 |
| A | THR100 |
| A | PHE239 |
| A | HOH1103 |
| A | GLY11 |
| A | ARG12 |
| A | MET13 |
| A | SER33 |
| A | GLU34 |
| A | ARG35 |
| A | PHE75 |
| A | THR76 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 1002 |
| Chain | Residue |
| A | HIS156 |
| A | LYS159 |
| A | ARG236 |
| A | SO41003 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 1003 |
| Chain | Residue |
| A | LYS159 |
| A | SER164 |
| A | GLY165 |
| A | THR166 |
| A | SO41002 |
| A | HOH1101 |
| A | HOH1109 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 1004 |
| Chain | Residue |
| A | ARG12 |
| A | ASN16 |
| A | ARG236 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 1005 |
| Chain | Residue |
| A | HIS158 |
| A | ARG236 |
| site_id | AC6 |
| Number of Residues | 22 |
| Details | binding site for residue NAD B 1001 |
| Chain | Residue |
| B | GLY8 |
| B | ALA10 |
| B | GLY11 |
| B | ARG12 |
| B | MET13 |
| B | SER33 |
| B | GLU34 |
| B | ARG35 |
| B | PHE75 |
| B | THR76 |
| B | SER80 |
| B | GLY98 |
| B | THR100 |
| B | ALA122 |
| B | PRO123 |
| B | ASN124 |
| B | TYR125 |
| B | LYS159 |
| B | PHE239 |
| B | 7FN1002 |
| B | HOH1108 |
| B | HOH1112 |
| site_id | AC7 |
| Number of Residues | 11 |
| Details | binding site for residue 7FN B 1002 |
| Chain | Residue |
| B | THR100 |
| B | PRO123 |
| B | HIS155 |
| B | HIS156 |
| B | LYS159 |
| B | SER164 |
| B | GLY165 |
| B | THR166 |
| B | NAD1001 |
| B | HOH1106 |
| B | HOH1111 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 1003 |
| Chain | Residue |
| B | ASN16 |
| B | ARG236 |
| site_id | AC9 |
| Number of Residues | 22 |
| Details | binding site for residue NAD C 1001 |
| Chain | Residue |
| C | GLY8 |
| C | GLY11 |
| C | ARG12 |
| C | MET13 |
| C | SER33 |
| C | GLU34 |
| C | ARG35 |
| C | PHE75 |
| C | THR76 |
| C | SER80 |
| C | GLY98 |
| C | THR100 |
| C | ALA122 |
| C | PRO123 |
| C | ASN124 |
| C | TYR125 |
| C | LYS159 |
| C | PHE239 |
| C | 7FN1002 |
| C | HOH1105 |
| C | HOH1108 |
| C | HOH1110 |
| site_id | AD1 |
| Number of Residues | 10 |
| Details | binding site for residue 7FN C 1002 |
| Chain | Residue |
| C | THR100 |
| C | PRO123 |
| C | HIS156 |
| C | LYS159 |
| C | SER164 |
| C | GLY165 |
| C | THR166 |
| C | NAD1001 |
| C | HOH1105 |
| C | HOH1110 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 C 1003 |
| Chain | Residue |
| C | ARG157 |
| C | HIS158 |
| site_id | AD3 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 C 1004 |
| Chain | Residue |
| C | ASN16 |
| C | ARG236 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 1005 |
| Chain | Residue |
| B | ILE223 |
| C | MET237 |
| C | THR238 |
| C | ASN241 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue 7FN C 1006 |
| Chain | Residue |
| C | HIS22 |
| C | LYS28 |
| C | VAL29 |
| C | LYS53 |
| C | PHE54 |
| site_id | AD6 |
| Number of Residues | 21 |
| Details | binding site for residue NAD D 1001 |
| Chain | Residue |
| D | GLY8 |
| D | GLY11 |
| D | ARG12 |
| D | MET13 |
| D | SER33 |
| D | GLU34 |
| D | ARG35 |
| D | PHE75 |
| D | THR76 |
| D | SER80 |
| D | GLY98 |
| D | THR100 |
| D | ALA122 |
| D | PRO123 |
| D | ASN124 |
| D | TYR125 |
| D | LYS159 |
| D | PHE239 |
| D | 7FN1002 |
| D | HOH1109 |
| D | HOH1114 |
| site_id | AD7 |
| Number of Residues | 11 |
| Details | binding site for residue 7FN D 1002 |
| Chain | Residue |
| D | THR100 |
| D | PRO123 |
| D | HIS155 |
| D | HIS156 |
| D | LYS159 |
| D | SER164 |
| D | GLY165 |
| D | THR166 |
| D | NAD1001 |
| D | HOH1109 |
| D | HOH1112 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 D 1003 |
| Chain | Residue |
| D | ARG12 |
| D | ASN16 |
| D | ARG236 |
| D | HOH1101 |
| site_id | AD9 |
| Number of Residues | 20 |
| Details | binding site for residue NAD E 1001 |
| Chain | Residue |
| E | GLY8 |
| E | ALA10 |
| E | GLY11 |
| E | ARG12 |
| E | MET13 |
| E | SER33 |
| E | GLU34 |
| E | PHE75 |
| E | THR76 |
| E | SER80 |
| E | GLY98 |
| E | THR100 |
| E | ALA122 |
| E | PRO123 |
| E | ASN124 |
| E | TYR125 |
| E | LYS159 |
| E | PHE239 |
| E | 7FN1002 |
| E | HOH1101 |
| site_id | AE1 |
| Number of Residues | 8 |
| Details | binding site for residue 7FN E 1002 |
| Chain | Residue |
| E | THR100 |
| E | PRO123 |
| E | HIS155 |
| E | HIS156 |
| E | LYS159 |
| E | GLY165 |
| E | THR166 |
| E | NAD1001 |
| site_id | AE2 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 E 1003 |
| Chain | Residue |
| E | ASP211 |
| E | ILE212 |
| E | VAL213 |
| E | GLY214 |
| E | ALA233 |
| E | THR234 |
| E | HOH1102 |
| F | ARG226 |
| G | THR234 |
| site_id | AE3 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 E 1004 |
| Chain | Residue |
| E | ASN16 |
| E | ARG236 |
| site_id | AE4 |
| Number of Residues | 21 |
| Details | binding site for residue NAD F 1001 |
| Chain | Residue |
| F | GLY8 |
| F | GLY11 |
| F | ARG12 |
| F | MET13 |
| F | SER33 |
| F | GLU34 |
| F | ARG35 |
| F | PHE75 |
| F | THR76 |
| F | SER80 |
| F | GLY98 |
| F | THR100 |
| F | ALA122 |
| F | PRO123 |
| F | ASN124 |
| F | TYR125 |
| F | LYS159 |
| F | PHE239 |
| F | 7FN1002 |
| F | HOH1102 |
| F | HOH1105 |
| site_id | AE5 |
| Number of Residues | 9 |
| Details | binding site for residue 7FN F 1002 |
| Chain | Residue |
| F | THR100 |
| F | PRO123 |
| F | HIS155 |
| F | HIS156 |
| F | LYS159 |
| F | GLY165 |
| F | THR166 |
| F | NAD1001 |
| F | HOH1103 |
| site_id | AE6 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 F 1003 |
| Chain | Residue |
| F | ASN16 |
| F | ARG236 |
| site_id | AE7 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 F 1004 |
| Chain | Residue |
| F | THR198 |
| F | LYS199 |
| site_id | AE8 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 F 1005 |
| Chain | Residue |
| F | PRO254 |
| site_id | AE9 |
| Number of Residues | 20 |
| Details | binding site for residue NAD G 1001 |
| Chain | Residue |
| G | GLY8 |
| G | ALA10 |
| G | GLY11 |
| G | ARG12 |
| G | MET13 |
| G | SER33 |
| G | GLU34 |
| G | ARG35 |
| G | PHE75 |
| G | THR76 |
| G | SER80 |
| G | GLY98 |
| G | THR100 |
| G | ALA122 |
| G | PRO123 |
| G | ASN124 |
| G | TYR125 |
| G | LYS159 |
| G | PHE239 |
| G | 7FN1002 |
| site_id | AF1 |
| Number of Residues | 10 |
| Details | binding site for residue 7FN G 1002 |
| Chain | Residue |
| G | THR100 |
| G | PRO123 |
| G | HIS155 |
| G | HIS156 |
| G | LYS159 |
| G | SER164 |
| G | GLY165 |
| G | THR166 |
| G | NAD1001 |
| G | HOH1103 |
| site_id | AF2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 G 1003 |
| Chain | Residue |
| G | ALA21 |
| G | HIS22 |
| G | LYS28 |
| G | VAL29 |
| G | PHE54 |
| site_id | AF3 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 G 1004 |
| Chain | Residue |
| G | THR100 |
| G | GLY101 |
| G | PHE102 |
| G | ARG107 |
| G | MET121 |
| G | GLY165 |
| site_id | AF4 |
| Number of Residues | 23 |
| Details | binding site for residue NAD H 1001 |
| Chain | Residue |
| H | GLY8 |
| H | GLY11 |
| H | ARG12 |
| H | MET13 |
| H | SER33 |
| H | GLU34 |
| H | ARG35 |
| H | PHE75 |
| H | THR76 |
| H | SER80 |
| H | GLY98 |
| H | THR100 |
| H | ALA122 |
| H | PRO123 |
| H | ASN124 |
| H | TYR125 |
| H | LYS159 |
| H | PHE239 |
| H | 7FN1002 |
| H | HOH1103 |
| H | HOH1104 |
| H | HOH1111 |
| H | HOH1120 |
| site_id | AF5 |
| Number of Residues | 11 |
| Details | binding site for residue 7FN H 1002 |
| Chain | Residue |
| H | THR100 |
| H | PRO123 |
| H | HIS155 |
| H | HIS156 |
| H | LYS159 |
| H | SER164 |
| H | GLY165 |
| H | THR166 |
| H | NAD1001 |
| H | HOH1104 |
| H | HOH1111 |
| site_id | AF6 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 H 1003 |
| Chain | Residue |
| H | THR100 |
| H | GLY101 |
| H | PHE102 |
| H | ARG107 |
| H | GLY165 |
| H | HOH1117 |
| site_id | AF7 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 H 1004 |
| Chain | Residue |
| H | ASN16 |
| H | ARG236 |
| site_id | AF8 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 H 1005 |
| Chain | Residue |
| H | MET237 |
| H | THR238 |
| H | ASN241 |
Functional Information from PROSITE/UniProt
| site_id | PS01298 |
| Number of Residues | 18 |
| Details | DAPB Dihydrodipicolinate reductase signature. EIvEaHhrhKvDapSGTA |
| Chain | Residue | Details |
| A | GLU150-ALA167 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000255|HAMAP-Rule:MF_00102 |
| Chain | Residue | Details |
| A | HIS155 | |
| B | HIS155 | |
| C | HIS155 | |
| D | HIS155 | |
| E | HIS155 | |
| F | HIS155 | |
| G | HIS155 | |
| H | HIS155 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | ACT_SITE: Proton donor => ECO:0000255|HAMAP-Rule:MF_00102 |
| Chain | Residue | Details |
| A | LYS159 | |
| B | LYS159 | |
| C | LYS159 | |
| D | LYS159 | |
| E | LYS159 | |
| F | LYS159 | |
| G | LYS159 | |
| H | LYS159 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 56 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00102 |
| Chain | Residue | Details |
| B | GLU34 | |
| B | ARG35 | |
| B | GLY98 | |
| B | ALA122 | |
| B | HIS156 | |
| B | GLY165 | |
| C | GLY8 | |
| C | GLU34 | |
| C | ARG35 | |
| C | GLY98 | |
| C | ALA122 | |
| C | HIS156 | |
| C | GLY165 | |
| D | GLY8 | |
| D | GLU34 | |
| D | ARG35 | |
| D | GLY98 | |
| D | ALA122 | |
| D | HIS156 | |
| D | GLY165 | |
| E | GLY8 | |
| E | GLU34 | |
| E | ARG35 | |
| E | GLY98 | |
| E | ALA122 | |
| E | HIS156 | |
| E | GLY165 | |
| F | GLY8 | |
| F | GLU34 | |
| F | ARG35 | |
| F | GLY98 | |
| F | ALA122 | |
| F | HIS156 | |
| F | GLY165 | |
| G | GLY8 | |
| G | GLU34 | |
| G | ARG35 | |
| G | GLY98 | |
| G | ALA122 | |
| G | HIS156 | |
| G | GLY165 | |
| H | GLY8 | |
| H | GLU34 | |
| H | ARG35 | |
| H | GLY98 | |
| H | ALA122 | |
| H | HIS156 | |
| H | GLY165 | |
| A | GLY8 | |
| A | GLU34 | |
| A | ARG35 | |
| A | GLY98 | |
| A | ALA122 | |
| A | HIS156 | |
| A | GLY165 | |
| B | GLY8 |
