3WBF
Crystal Structure of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum co-crystallized with NADP+ and DAP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0019877 | biological_process | diaminopimelate biosynthetic process |
| A | 0047850 | molecular_function | diaminopimelate dehydrogenase activity |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0009085 | biological_process | lysine biosynthetic process |
| B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0019877 | biological_process | diaminopimelate biosynthetic process |
| B | 0047850 | molecular_function | diaminopimelate dehydrogenase activity |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0009085 | biological_process | lysine biosynthetic process |
| C | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0019877 | biological_process | diaminopimelate biosynthetic process |
| C | 0047850 | molecular_function | diaminopimelate dehydrogenase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE API A 301 |
| Chain | Residue |
| A | ASP92 |
| A | ASN253 |
| A | NAP308 |
| A | HOH528 |
| A | HOH706 |
| A | ASP122 |
| A | SER151 |
| A | MET152 |
| A | GLY153 |
| A | HIS154 |
| A | THR171 |
| A | ARG181 |
| A | HIS227 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 302 |
| Chain | Residue |
| A | SER56 |
| A | ARG83 |
| A | GOL303 |
| A | HOH579 |
| A | HOH863 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 303 |
| Chain | Residue |
| A | ARG5 |
| A | GLY60 |
| A | VAL61 |
| A | ARG83 |
| A | GOL302 |
| A | HOH670 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL A 304 |
| Chain | Residue |
| A | LYS3 |
| A | VAL22 |
| A | GLN23 |
| A | ALA25 |
| A | MET28 |
| A | HOH470 |
| A | HOH686 |
| A | HOH687 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL A 305 |
| Chain | Residue |
| A | GLU248 |
| C | GOL303 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL A 306 |
| Chain | Residue |
| A | ARG270 |
| A | GLN271 |
| A | HOH411 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL A 307 |
| Chain | Residue |
| A | ARG246 |
| A | GLU248 |
| A | HOH703 |
| site_id | AC8 |
| Number of Residues | 36 |
| Details | BINDING SITE FOR RESIDUE NAP A 308 |
| Chain | Residue |
| A | GLY10 |
| A | TYR11 |
| A | GLY12 |
| A | ASN13 |
| A | VAL14 |
| A | ARG35 |
| A | ARG36 |
| A | CYS67 |
| A | VAL68 |
| A | PRO69 |
| A | THR70 |
| A | TYR76 |
| A | SER90 |
| A | ASP92 |
| A | GLY120 |
| A | TRP121 |
| A | ASP122 |
| A | PRO123 |
| A | MET152 |
| A | GLY153 |
| A | VAL156 |
| A | LYS159 |
| A | ASN253 |
| A | THR257 |
| A | API301 |
| A | HOH448 |
| A | HOH451 |
| A | HOH452 |
| A | HOH466 |
| A | HOH479 |
| A | HOH487 |
| A | HOH495 |
| A | HOH618 |
| A | HOH662 |
| A | HOH664 |
| A | HOH884 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE API B 301 |
| Chain | Residue |
| B | ASP92 |
| B | ASP122 |
| B | PHE146 |
| B | SER151 |
| B | MET152 |
| B | GLY153 |
| B | HIS154 |
| B | THR171 |
| B | ARG181 |
| B | HIS227 |
| B | ASN253 |
| B | NAP306 |
| B | HOH442 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 302 |
| Chain | Residue |
| B | ILE55 |
| B | ARG83 |
| B | ILE85 |
| C | GOL305 |
| site_id | BC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL B 303 |
| Chain | Residue |
| C | PRO138 |
| C | LYS139 |
| C | VAL236 |
| C | GLY238 |
| B | ALA21 |
| B | ALA24 |
| B | ALA25 |
| B | GLN259 |
| B | HOH432 |
| B | HOH539 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL B 304 |
| Chain | Residue |
| B | HIS94 |
| B | ARG130 |
| B | HOH621 |
| site_id | BC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 305 |
| Chain | Residue |
| B | ARG270 |
| B | GLY289 |
| B | ASP290 |
| B | HOH409 |
| B | HOH430 |
| B | HOH587 |
| B | HOH610 |
| site_id | BC5 |
| Number of Residues | 37 |
| Details | BINDING SITE FOR RESIDUE NAP B 306 |
| Chain | Residue |
| B | GLY10 |
| B | TYR11 |
| B | GLY12 |
| B | ASN13 |
| B | VAL14 |
| B | ARG35 |
| B | ARG36 |
| B | CYS67 |
| B | VAL68 |
| B | PRO69 |
| B | THR70 |
| B | SER72 |
| B | TYR76 |
| B | SER90 |
| B | ASP92 |
| B | GLY120 |
| B | TRP121 |
| B | ASP122 |
| B | PRO123 |
| B | MET152 |
| B | GLY153 |
| B | VAL156 |
| B | LYS159 |
| B | ASN253 |
| B | THR257 |
| B | API301 |
| B | HOH412 |
| B | HOH436 |
| B | HOH494 |
| B | HOH535 |
| B | HOH561 |
| B | HOH579 |
| B | HOH609 |
| B | HOH675 |
| B | HOH689 |
| B | HOH690 |
| B | HOH691 |
| site_id | BC6 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE API C 301 |
| Chain | Residue |
| C | ASP92 |
| C | ASP122 |
| C | PHE146 |
| C | SER151 |
| C | MET152 |
| C | GLY153 |
| C | HIS154 |
| C | THR171 |
| C | ARG181 |
| C | HIS227 |
| C | ASN253 |
| C | NAP308 |
| C | HOH562 |
| C | HOH583 |
| C | HOH604 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL C 302 |
| Chain | Residue |
| C | ARG5 |
| C | GLY60 |
| C | GLN62 |
| C | HOH488 |
| C | HOH678 |
| C | HOH698 |
| site_id | BC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL C 303 |
| Chain | Residue |
| A | GOL305 |
| C | GLU248 |
| site_id | BC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL C 304 |
| Chain | Residue |
| C | GLU248 |
| C | ARG250 |
| C | HOH588 |
| C | HOH603 |
| C | HOH619 |
| site_id | CC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL C 305 |
| Chain | Residue |
| B | VAL61 |
| B | GLY84 |
| B | GOL302 |
| C | HOH440 |
| site_id | CC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL C 306 |
| Chain | Residue |
| C | ASP27 |
| C | ARG266 |
| C | ALA269 |
| C | ARG270 |
| C | PRO288 |
| C | GLY289 |
| C | HOH537 |
| C | HOH573 |
| C | HOH802 |
| site_id | CC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL C 307 |
| Chain | Residue |
| A | ARG50 |
| C | PRO273 |
| C | HOH529 |
| C | HOH563 |
| C | HOH852 |
| site_id | CC4 |
| Number of Residues | 34 |
| Details | BINDING SITE FOR RESIDUE NAP C 308 |
| Chain | Residue |
| C | GLY10 |
| C | TYR11 |
| C | GLY12 |
| C | ASN13 |
| C | VAL14 |
| C | ARG35 |
| C | ARG36 |
| C | CYS67 |
| C | VAL68 |
| C | PRO69 |
| C | THR70 |
| C | TYR76 |
| C | SER90 |
| C | ASP92 |
| C | GLY120 |
| C | TRP121 |
| C | ASP122 |
| C | PRO123 |
| C | MET152 |
| C | GLY153 |
| C | VAL156 |
| C | ASN253 |
| C | THR257 |
| C | API301 |
| C | HOH415 |
| C | HOH423 |
| C | HOH448 |
| C | HOH456 |
| C | HOH475 |
| C | HOH496 |
| C | HOH560 |
| C | HOH569 |
| C | HOH582 |
| C | HOH635 |
