5V96
Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with bound NAD and Adenosine
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0004013 | molecular_function | adenosylhomocysteinase activity |
| A | 0005829 | cellular_component | cytosol |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0033353 | biological_process | S-adenosylmethionine cycle |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0004013 | molecular_function | adenosylhomocysteinase activity |
| B | 0005829 | cellular_component | cytosol |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0033353 | biological_process | S-adenosylmethionine cycle |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0004013 | molecular_function | adenosylhomocysteinase activity |
| C | 0005829 | cellular_component | cytosol |
| C | 0006730 | biological_process | one-carbon metabolic process |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0033353 | biological_process | S-adenosylmethionine cycle |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0004013 | molecular_function | adenosylhomocysteinase activity |
| D | 0005829 | cellular_component | cytosol |
| D | 0006730 | biological_process | one-carbon metabolic process |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0033353 | biological_process | S-adenosylmethionine cycle |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 34 |
| Details | binding site for residue NAD A 501 |
| Chain | Residue |
| A | THR198 |
| A | GLU284 |
| A | ILE285 |
| A | ASP286 |
| A | ASN289 |
| A | ALA316 |
| A | THR317 |
| A | GLY318 |
| A | ASN319 |
| A | ILE322 |
| A | ILE340 |
| A | THR199 |
| A | GLY341 |
| A | HIS342 |
| A | ASN388 |
| A | HIS395 |
| A | ADN502 |
| A | HOH682 |
| A | HOH709 |
| A | HOH720 |
| A | HOH735 |
| A | HOH739 |
| A | THR200 |
| A | HOH760 |
| A | HOH837 |
| B | GLN453 |
| B | LYS466 |
| B | TYR470 |
| A | ASN232 |
| A | GLY261 |
| A | GLY263 |
| A | ASP264 |
| A | VAL265 |
| A | THR283 |
| site_id | AC2 |
| Number of Residues | 17 |
| Details | binding site for residue ADN A 502 |
| Chain | Residue |
| A | LEU58 |
| A | HIS59 |
| A | THR61 |
| A | GLU63 |
| A | THR64 |
| A | ASP136 |
| A | GLU197 |
| A | THR198 |
| A | LYS227 |
| A | ASP231 |
| A | THR393 |
| A | GLY394 |
| A | HIS395 |
| A | MET400 |
| A | PHE404 |
| A | NAD501 |
| A | PO4503 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | binding site for residue PO4 A 503 |
| Chain | Residue |
| A | HIS59 |
| A | CYS83 |
| A | ASN84 |
| A | HIS342 |
| A | PHE343 |
| A | LEU386 |
| A | ADN502 |
| A | HOH632 |
| A | HOH688 |
| A | HOH704 |
| A | HOH709 |
| A | HOH866 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 504 |
| Chain | Residue |
| A | ARG246 |
| A | HOH859 |
| D | ARG246 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 505 |
| Chain | Residue |
| A | ILE457 |
| A | TYR465 |
| B | HIS203 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 506 |
| Chain | Residue |
| A | PRO464 |
| A | HOH870 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 507 |
| Chain | Residue |
| A | HIS469 |
| A | ARG471 |
| A | HOH811 |
| B | ASP223 |
| B | HOH772 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 508 |
| Chain | Residue |
| A | LYS42 |
| A | GLU433 |
| A | HOH610 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 509 |
| Chain | Residue |
| A | ASN84 |
| A | ILE85 |
| A | LEU111 |
| A | TYR114 |
| A | GLU165 |
| A | ARG385 |
| A | HOH624 |
| A | HOH846 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 510 |
| Chain | Residue |
| A | TYR424 |
| A | THR425 |
| A | HOH627 |
| A | HOH648 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 511 |
| Chain | Residue |
| A | GLU116 |
| A | TRP119 |
| A | ARG175 |
| A | GLU179 |
| D | PRO126 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 512 |
| Chain | Residue |
| A | HOH624 |
| A | ASP139 |
| A | LEU142 |
| A | ARG204 |
| site_id | AD4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 513 |
| Chain | Residue |
| A | ARG204 |
| A | HOH723 |
| B | TYR456 |
| site_id | AD5 |
| Number of Residues | 33 |
| Details | binding site for residue NAD B 501 |
| Chain | Residue |
| A | GLN453 |
| A | LYS466 |
| A | TYR470 |
| B | THR198 |
| B | THR199 |
| B | THR200 |
| B | ASN232 |
| B | GLY263 |
| B | ASP264 |
| B | VAL265 |
| B | THR283 |
| B | GLU284 |
| B | ILE285 |
| B | ASP286 |
| B | ASN289 |
| B | ALA316 |
| B | THR317 |
| B | GLY318 |
| B | ASN319 |
| B | ILE322 |
| B | ILE340 |
| B | GLY341 |
| B | HIS342 |
| B | ASN388 |
| B | HIS395 |
| B | ADN502 |
| B | HOH718 |
| B | HOH757 |
| B | HOH759 |
| B | HOH768 |
| B | HOH785 |
| B | HOH806 |
| B | HOH900 |
| site_id | AD6 |
| Number of Residues | 16 |
| Details | binding site for residue ADN B 502 |
| Chain | Residue |
| B | LEU58 |
| B | HIS59 |
| B | THR61 |
| B | GLU63 |
| B | THR64 |
| B | ASP136 |
| B | GLU197 |
| B | THR198 |
| B | LYS227 |
| B | ASP231 |
| B | THR393 |
| B | HIS395 |
| B | MET400 |
| B | PHE404 |
| B | NAD501 |
| B | PO4503 |
| site_id | AD7 |
| Number of Residues | 11 |
| Details | binding site for residue PO4 B 503 |
| Chain | Residue |
| B | HIS59 |
| B | CYS83 |
| B | ASN84 |
| B | HIS342 |
| B | PHE343 |
| B | LEU386 |
| B | ADN502 |
| B | HOH608 |
| B | HOH730 |
| B | HOH736 |
| B | HOH768 |
| site_id | AD8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 504 |
| Chain | Residue |
| A | LYS152 |
| B | VAL13 |
| B | TRP106 |
| site_id | AD9 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 505 |
| Chain | Residue |
| B | ARG123 |
| B | PRO126 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 506 |
| Chain | Residue |
| A | TYR456 |
| A | HOH660 |
| B | HIS203 |
| B | ARG204 |
| site_id | AE2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 507 |
| Chain | Residue |
| B | ARG246 |
| C | ARG246 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 508 |
| Chain | Residue |
| B | GLU433 |
| B | LEU437 |
| B | HOH612 |
| B | HOH742 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 509 |
| Chain | Residue |
| B | ASN50 |
| B | GLY51 |
| B | VAL52 |
| B | GLN131 |
| B | TRP415 |
| B | EDO510 |
| site_id | AE5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 510 |
| Chain | Residue |
| B | ARG53 |
| B | ASP190 |
| B | EDO509 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 511 |
| Chain | Residue |
| B | LYS152 |
| B | SER185 |
| C | TRP415 |
| C | HOH715 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 512 |
| Chain | Residue |
| B | ASP158 |
| B | GLU159 |
| B | ASP160 |
| B | GLY161 |
| site_id | AE8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 513 |
| Chain | Residue |
| B | LEU142 |
| B | GLU165 |
| B | HOH690 |
| site_id | AE9 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 514 |
| Chain | Residue |
| B | LYS418 |
| B | TYR419 |
| site_id | AF1 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 515 |
| Chain | Residue |
| B | CYS83 |
| B | ASN84 |
| B | ILE85 |
| B | LEU111 |
| B | TYR114 |
| B | ARG385 |
| B | HOH610 |
| B | HOH717 |
| site_id | AF2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 516 |
| Chain | Residue |
| A | HIS203 |
| B | ILE457 |
| B | TYR465 |
| B | HOH873 |
| site_id | AF3 |
| Number of Residues | 33 |
| Details | binding site for residue NAD C 501 |
| Chain | Residue |
| C | THR198 |
| C | THR199 |
| C | THR200 |
| C | ASN232 |
| C | GLY261 |
| C | GLY263 |
| C | ASP264 |
| C | VAL265 |
| C | THR283 |
| C | GLU284 |
| C | ILE285 |
| C | ASP286 |
| C | ASN289 |
| C | ALA316 |
| C | THR317 |
| C | GLY318 |
| C | ASN319 |
| C | ILE322 |
| C | ILE340 |
| C | GLY341 |
| C | HIS342 |
| C | ASN388 |
| C | HIS395 |
| C | ADN502 |
| C | HOH671 |
| C | HOH709 |
| C | HOH728 |
| C | HOH772 |
| C | HOH796 |
| C | HOH810 |
| D | GLN453 |
| D | LYS466 |
| D | TYR470 |
| site_id | AF4 |
| Number of Residues | 15 |
| Details | binding site for residue ADN C 502 |
| Chain | Residue |
| C | HIS59 |
| C | THR61 |
| C | GLU63 |
| C | THR64 |
| C | ASP136 |
| C | GLU197 |
| C | THR198 |
| C | LYS227 |
| C | ASP231 |
| C | THR393 |
| C | HIS395 |
| C | MET400 |
| C | PHE404 |
| C | NAD501 |
| C | PO4503 |
| site_id | AF5 |
| Number of Residues | 11 |
| Details | binding site for residue PO4 C 503 |
| Chain | Residue |
| C | HIS59 |
| C | CYS83 |
| C | ASN84 |
| C | HIS342 |
| C | PHE343 |
| C | LEU386 |
| C | ADN502 |
| C | HOH610 |
| C | HOH619 |
| C | HOH642 |
| C | HOH723 |
| site_id | AF6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 504 |
| Chain | Residue |
| C | ARG123 |
| C | PRO126 |
| site_id | AF7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 505 |
| Chain | Residue |
| B | LYS274 |
| C | ARG237 |
| C | GLU271 |
| C | HOH638 |
| D | ALA296 |
| site_id | AF8 |
| Number of Residues | 8 |
| Details | binding site for residue EDO C 506 |
| Chain | Residue |
| C | CYS83 |
| C | ASN84 |
| C | ILE85 |
| C | LEU111 |
| C | TYR114 |
| C | ARG385 |
| C | HOH653 |
| C | HOH657 |
| site_id | AF9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 507 |
| Chain | Residue |
| C | ARG146 |
| C | GLN149 |
| C | MET208 |
| C | HOH646 |
| C | HOH674 |
| site_id | AG1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 508 |
| Chain | Residue |
| C | ARG204 |
| C | HOH886 |
| site_id | AG2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 509 |
| Chain | Residue |
| C | ALA38 |
| C | CYS39 |
| C | LYS42 |
| C | TYR43 |
| C | GLU433 |
| C | LEU437 |
| site_id | AG3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 510 |
| Chain | Residue |
| C | ILE457 |
| C | TYR465 |
| C | HOH786 |
| D | HIS203 |
| site_id | AG4 |
| Number of Residues | 1 |
| Details | binding site for residue EDO C 511 |
| Chain | Residue |
| C | ASN460 |
| site_id | AG5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 512 |
| Chain | Residue |
| C | PRO427 |
| C | LYS428 |
| C | HOH605 |
| site_id | AG6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 513 |
| Chain | Residue |
| C | ASP417 |
| C | LYS418 |
| C | TYR419 |
| site_id | AG7 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 514 |
| Chain | Residue |
| C | LYS320 |
| D | SER452 |
| site_id | AG8 |
| Number of Residues | 34 |
| Details | binding site for residue NAD D 501 |
| Chain | Residue |
| C | LYS466 |
| C | TYR470 |
| D | THR198 |
| D | THR199 |
| D | THR200 |
| D | ASN232 |
| D | GLY261 |
| D | GLY263 |
| D | ASP264 |
| D | VAL265 |
| D | THR283 |
| D | GLU284 |
| D | ILE285 |
| D | ASP286 |
| D | ASN289 |
| D | ALA316 |
| D | THR317 |
| D | GLY318 |
| D | ASN319 |
| D | ILE322 |
| D | ILE340 |
| D | GLY341 |
| D | HIS342 |
| D | LEU386 |
| D | ASN388 |
| D | HIS395 |
| D | ADN502 |
| D | HOH693 |
| D | HOH731 |
| D | HOH734 |
| D | HOH764 |
| D | HOH803 |
| D | HOH806 |
| D | HOH826 |
| site_id | AG9 |
| Number of Residues | 15 |
| Details | binding site for residue ADN D 502 |
| Chain | Residue |
| D | HIS59 |
| D | THR61 |
| D | GLU63 |
| D | THR64 |
| D | ASP136 |
| D | GLU197 |
| D | THR198 |
| D | LYS227 |
| D | ASP231 |
| D | THR393 |
| D | HIS395 |
| D | MET400 |
| D | PHE404 |
| D | NAD501 |
| D | PO4503 |
| site_id | AH1 |
| Number of Residues | 11 |
| Details | binding site for residue PO4 D 503 |
| Chain | Residue |
| D | HIS59 |
| D | CYS83 |
| D | ASN84 |
| D | HIS342 |
| D | PHE343 |
| D | LEU386 |
| D | ADN502 |
| D | HOH635 |
| D | HOH639 |
| D | HOH731 |
| D | HOH756 |
| site_id | AH2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 504 |
| Chain | Residue |
| A | LEU21 |
| D | PRO365 |
| D | HOH608 |
| D | HOH836 |
| site_id | AH3 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 505 |
| Chain | Residue |
| C | HIS469 |
| D | HIS469 |
| site_id | AH4 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 506 |
| Chain | Residue |
| D | GLN149 |
| D | HOH748 |
| site_id | AH5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 507 |
| Chain | Residue |
| C | THR425 |
| D | HIS469 |
| D | HOH736 |
| D | HOH813 |
| site_id | AH6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 508 |
| Chain | Residue |
| D | GLN12 |
| D | TRP106 |
| site_id | AH7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 509 |
| Chain | Residue |
| D | ALA38 |
| D | LYS42 |
| D | GLU433 |
| D | LEU437 |
| D | HOH607 |
| D | HOH760 |
| site_id | AH8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 510 |
| Chain | Residue |
| D | ASN50 |
| D | GLY51 |
| D | VAL52 |
| D | ARG53 |
| D | GLN131 |
| D | EDO514 |
| site_id | AH9 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 511 |
| Chain | Residue |
| D | ASN84 |
| D | ILE85 |
| D | TYR114 |
| D | GLU165 |
| D | ARG385 |
| D | HOH654 |
| D | HOH704 |
| site_id | AI1 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 512 |
| Chain | Residue |
| A | PRO126 |
| D | GLU116 |
| D | TRP119 |
| D | ARG175 |
| D | GLU179 |
| D | HOH714 |
| D | HOH783 |
| site_id | AI2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 513 |
| Chain | Residue |
| D | PRO189 |
| D | HOH650 |
| D | HOH805 |
| site_id | AI3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 514 |
| Chain | Residue |
| D | ARG53 |
| D | ASP190 |
| D | EDO510 |
| site_id | AI4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 515 |
| Chain | Residue |
| D | PRO464 |
| D | LYS466 |
| D | ALA467 |
Functional Information from PROSITE/UniProt
| site_id | PS00738 |
| Number of Residues | 15 |
| Details | ADOHCYASE_1 S-adenosyl-L-homocysteine hydrolase signature 1. SCNiFSTQDdAAAAI |
| Chain | Residue | Details |
| A | SER82-ILE96 |
| site_id | PS00739 |
| Number of Residues | 17 |
| Details | ADOHCYASE_2 S-adenosyl-L-homocysteine hydrolase signature 2. GKecvIcGFGdVGKGc.A |
| Chain | Residue | Details |
| A | GLY254-ALA270 |
