7DO5
Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase(apo-form)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0006633 | biological_process | fatty acid biosynthetic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| A | 0019299 | biological_process | rhamnose metabolic process |
| A | 0019301 | biological_process | rhamnose catabolic process |
| A | 0048038 | molecular_function | quinone binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0006633 | biological_process | fatty acid biosynthetic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| B | 0019299 | biological_process | rhamnose metabolic process |
| B | 0019301 | biological_process | rhamnose catabolic process |
| B | 0048038 | molecular_function | quinone binding |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0006633 | biological_process | fatty acid biosynthetic process |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| C | 0019299 | biological_process | rhamnose metabolic process |
| C | 0019301 | biological_process | rhamnose catabolic process |
| C | 0048038 | molecular_function | quinone binding |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0006633 | biological_process | fatty acid biosynthetic process |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| D | 0019299 | biological_process | rhamnose metabolic process |
| D | 0019301 | biological_process | rhamnose catabolic process |
| D | 0048038 | molecular_function | quinone binding |
| E | 0000166 | molecular_function | nucleotide binding |
| E | 0006633 | biological_process | fatty acid biosynthetic process |
| E | 0016491 | molecular_function | oxidoreductase activity |
| E | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| E | 0019299 | biological_process | rhamnose metabolic process |
| E | 0019301 | biological_process | rhamnose catabolic process |
| E | 0048038 | molecular_function | quinone binding |
| F | 0000166 | molecular_function | nucleotide binding |
| F | 0006633 | biological_process | fatty acid biosynthetic process |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| F | 0019299 | biological_process | rhamnose metabolic process |
| F | 0019301 | biological_process | rhamnose catabolic process |
| F | 0048038 | molecular_function | quinone binding |
| G | 0000166 | molecular_function | nucleotide binding |
| G | 0006633 | biological_process | fatty acid biosynthetic process |
| G | 0016491 | molecular_function | oxidoreductase activity |
| G | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| G | 0019299 | biological_process | rhamnose metabolic process |
| G | 0019301 | biological_process | rhamnose catabolic process |
| G | 0048038 | molecular_function | quinone binding |
| H | 0000166 | molecular_function | nucleotide binding |
| H | 0006633 | biological_process | fatty acid biosynthetic process |
| H | 0016491 | molecular_function | oxidoreductase activity |
| H | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| H | 0019299 | biological_process | rhamnose metabolic process |
| H | 0019301 | biological_process | rhamnose catabolic process |
| H | 0048038 | molecular_function | quinone binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 301 |
| Chain | Residue |
| A | ARG43 |
| A | GLY64 |
| A | LYS75 |
| A | HOH428 |
| A | HOH489 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 302 |
| Chain | Residue |
| A | SER37 |
| A | GLY42 |
| A | HOH435 |
| A | GLY12 |
| A | ALA13 |
| A | SER14 |
| A | HIS36 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 303 |
| Chain | Residue |
| A | LYS206 |
| A | ARG209 |
| A | ARG213 |
| site_id | AC4 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 B 301 |
| Chain | Residue |
| B | GLY12 |
| B | ALA13 |
| B | SER14 |
| B | HIS36 |
| B | SER37 |
| B | GLY42 |
| B | HOH403 |
| B | HOH425 |
| B | HOH428 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 302 |
| Chain | Residue |
| B | ARG43 |
| B | GLY64 |
| B | HOH410 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 303 |
| Chain | Residue |
| B | ARG209 |
| B | ARG213 |
| site_id | AC7 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 C 301 |
| Chain | Residue |
| C | GLY12 |
| C | ALA13 |
| C | SER14 |
| C | HIS36 |
| C | SER37 |
| C | GLY42 |
| C | HOH454 |
| C | HOH547 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 302 |
| Chain | Residue |
| C | GLY64 |
| C | LYS75 |
| C | HOH462 |
| C | HOH489 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 C 303 |
| Chain | Residue |
| C | LYS206 |
| C | ARG209 |
| C | ARG213 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 D 301 |
| Chain | Residue |
| D | GLY12 |
| D | ALA13 |
| D | SER14 |
| D | HIS36 |
| D | SER37 |
| D | GLY42 |
| D | HOH414 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 D 302 |
| Chain | Residue |
| D | ARG43 |
| D | GLY64 |
| D | HOH454 |
| D | HOH495 |
| site_id | AD3 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 D 303 |
| Chain | Residue |
| D | ARG209 |
| site_id | AD4 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 E 301 |
| Chain | Residue |
| E | GLY12 |
| E | ALA13 |
| E | SER14 |
| E | HIS36 |
| E | SER37 |
| E | GLY42 |
| E | HOH406 |
| E | HOH423 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 E 302 |
| Chain | Residue |
| E | ARG43 |
| E | VAL63 |
| E | GLY64 |
| E | HOH512 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 E 303 |
| Chain | Residue |
| E | LYS206 |
| E | ARG209 |
| G | HOH411 |
| site_id | AD7 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 F 301 |
| Chain | Residue |
| F | GLY12 |
| F | ALA13 |
| F | SER14 |
| F | HIS36 |
| F | SER37 |
| F | GLY42 |
| F | HOH466 |
| F | HOH483 |
| site_id | AD8 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 F 302 |
| Chain | Residue |
| F | ARG43 |
| F | VAL63 |
| F | GLY64 |
| F | LYS75 |
| F | HOH423 |
| site_id | AD9 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 F 303 |
| Chain | Residue |
| F | LYS206 |
| F | ARG209 |
| site_id | AE1 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 G 301 |
| Chain | Residue |
| G | GLY12 |
| G | ALA13 |
| G | SER14 |
| G | HIS36 |
| G | SER37 |
| G | GLY42 |
| G | HOH407 |
| G | HOH476 |
| G | HOH512 |
| site_id | AE2 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 G 302 |
| Chain | Residue |
| G | ARG43 |
| G | GLY64 |
| G | HOH412 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 G 303 |
| Chain | Residue |
| G | ARG209 |
| G | ARG213 |
| G | LYS206 |
| site_id | AE4 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 H 301 |
| Chain | Residue |
| H | GLY12 |
| H | ALA13 |
| H | SER14 |
| H | HIS36 |
| H | SER37 |
| H | GLY42 |
| H | HOH447 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 H 302 |
| Chain | Residue |
| H | ARG43 |
| H | GLY64 |
| H | HOH404 |
| H | HOH405 |
| H | HOH429 |
| site_id | AE6 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 H 303 |
| Chain | Residue |
| H | ARG209 |
| H | ARG213 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | ACT_SITE: Proton donor => ECO:0000250|UniProtKB:O93868 |
| Chain | Residue | Details |
| A | SER146 | |
| B | SER146 | |
| C | SER146 | |
| D | SER146 | |
| E | SER146 | |
| F | SER146 | |
| G | SER146 | |
| H | SER146 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:O93868 |
| Chain | Residue | Details |
| A | TYR159 | |
| B | TYR159 | |
| C | TYR159 | |
| D | TYR159 | |
| E | TYR159 | |
| F | TYR159 | |
| G | TYR159 | |
| H | TYR159 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | ACT_SITE: Lowers pKa of active site Tyr => ECO:0000250|UniProtKB:O93868 |
| Chain | Residue | Details |
| A | LYS163 | |
| B | LYS163 | |
| C | LYS163 | |
| D | LYS163 | |
| E | LYS163 | |
| F | LYS163 | |
| G | LYS163 | |
| H | LYS163 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 80 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:33482017, ECO:0007744|PDB:7B81, ECO:0007744|PDB:7DO6, ECO:0007744|PDB:7DO7 |
| Chain | Residue | Details |
| A | GLY12 | |
| A | ILE192 | |
| B | GLY12 | |
| B | SER14 | |
| B | ARG15 | |
| B | ILE17 | |
| B | ASP66 | |
| B | ALA67 | |
| B | ASN93 | |
| B | TYR159 | |
| B | LYS163 | |
| A | SER14 | |
| B | ILE192 | |
| C | GLY12 | |
| C | SER14 | |
| C | ARG15 | |
| C | ILE17 | |
| C | ASP66 | |
| C | ALA67 | |
| C | ASN93 | |
| C | TYR159 | |
| C | LYS163 | |
| A | ARG15 | |
| C | ILE192 | |
| D | GLY12 | |
| D | SER14 | |
| D | ARG15 | |
| D | ILE17 | |
| D | ASP66 | |
| D | ALA67 | |
| D | ASN93 | |
| D | TYR159 | |
| D | LYS163 | |
| A | ILE17 | |
| D | ILE192 | |
| E | GLY12 | |
| E | SER14 | |
| E | ARG15 | |
| E | ILE17 | |
| E | ASP66 | |
| E | ALA67 | |
| E | ASN93 | |
| E | TYR159 | |
| E | LYS163 | |
| A | ASP66 | |
| E | ILE192 | |
| F | GLY12 | |
| F | SER14 | |
| F | ARG15 | |
| F | ILE17 | |
| F | ASP66 | |
| F | ALA67 | |
| F | ASN93 | |
| F | TYR159 | |
| F | LYS163 | |
| A | ALA67 | |
| F | ILE192 | |
| G | GLY12 | |
| G | SER14 | |
| G | ARG15 | |
| G | ILE17 | |
| G | ASP66 | |
| G | ALA67 | |
| G | ASN93 | |
| G | TYR159 | |
| G | LYS163 | |
| A | ASN93 | |
| G | ILE192 | |
| H | GLY12 | |
| H | SER14 | |
| H | ARG15 | |
| H | ILE17 | |
| H | ASP66 | |
| H | ALA67 | |
| H | ASN93 | |
| H | TYR159 | |
| H | LYS163 | |
| A | TYR159 | |
| H | ILE192 | |
| A | LYS163 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:33482017, ECO:0007744|PDB:7DO6 |
| Chain | Residue | Details |
| A | SER37 | |
| B | SER37 | |
| C | SER37 | |
| D | SER37 | |
| E | SER37 | |
| F | SER37 | |
| G | SER37 | |
| H | SER37 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 40 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:33482017, ECO:0007744|PDB:7DO7 |
| Chain | Residue | Details |
| A | SER146 | |
| B | ASN197 | |
| C | SER146 | |
| C | SER148 | |
| C | GLN156 | |
| C | THR191 | |
| C | ASN197 | |
| D | SER146 | |
| D | SER148 | |
| D | GLN156 | |
| D | THR191 | |
| A | SER148 | |
| D | ASN197 | |
| E | SER146 | |
| E | SER148 | |
| E | GLN156 | |
| E | THR191 | |
| E | ASN197 | |
| F | SER146 | |
| F | SER148 | |
| F | GLN156 | |
| F | THR191 | |
| A | GLN156 | |
| F | ASN197 | |
| G | SER146 | |
| G | SER148 | |
| G | GLN156 | |
| G | THR191 | |
| G | ASN197 | |
| H | SER146 | |
| H | SER148 | |
| H | GLN156 | |
| H | THR191 | |
| A | THR191 | |
| H | ASN197 | |
| A | ASN197 | |
| B | SER146 | |
| B | SER148 | |
| B | GLN156 | |
| B | THR191 |
