6AOC
Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003676 | molecular_function | nucleic acid binding |
| A | 0003964 | molecular_function | RNA-directed DNA polymerase activity |
| A | 0004523 | molecular_function | RNA-DNA hybrid ribonuclease activity |
| A | 0006278 | biological_process | RNA-templated DNA biosynthetic process |
| B | 0003964 | molecular_function | RNA-directed DNA polymerase activity |
| B | 0006278 | biological_process | RNA-templated DNA biosynthetic process |
| C | 0003676 | molecular_function | nucleic acid binding |
| C | 0003964 | molecular_function | RNA-directed DNA polymerase activity |
| C | 0004523 | molecular_function | RNA-DNA hybrid ribonuclease activity |
| C | 0006278 | biological_process | RNA-templated DNA biosynthetic process |
| D | 0003964 | molecular_function | RNA-directed DNA polymerase activity |
| D | 0006278 | biological_process | RNA-templated DNA biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue MN A 601 |
| Chain | Residue |
| A | ASP443 |
| A | GLU478 |
| A | ASP498 |
| A | ZW2603 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MN A 602 |
| Chain | Residue |
| A | ASP443 |
| A | ASP549 |
| A | ZW2603 |
| A | HOH777 |
| A | HOH783 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | binding site for residue ZW2 A 603 |
| Chain | Residue |
| A | ASP443 |
| A | GLU478 |
| A | ASP498 |
| A | HIS539 |
| A | ASP549 |
| A | MN601 |
| A | MN602 |
| A | HOH730 |
| A | HOH742 |
| A | HOH777 |
| A | HOH783 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue PGE A 604 |
| Chain | Residue |
| A | GLN394 |
| A | LYS395 |
| A | GLU396 |
| A | PHE416 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 605 |
| Chain | Residue |
| A | PHE389 |
| A | GLU413 |
| A | GLU415 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 606 |
| Chain | Residue |
| A | LYS101 |
| A | LYS102 |
| A | LYS103 |
| A | VAL106 |
| A | TYR188 |
| A | PRO236 |
| A | TYR318 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 607 |
| Chain | Residue |
| A | LYS461 |
| A | ARG463 |
| C | PRO468 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 608 |
| Chain | Residue |
| A | LYS281 |
| A | ARG284 |
| C | LYS70 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 609 |
| Chain | Residue |
| A | GLN373 |
| A | THR377 |
| A | HOH739 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 610 |
| Chain | Residue |
| A | THR403 |
| A | GLU404 |
| A | TYR405 |
| B | LYS331 |
| B | LYS424 |
| site_id | AD2 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 611 |
| Chain | Residue |
| A | ALA437 |
| A | GLU438 |
| A | ASN460 |
| A | LYS461 |
| A | HOH710 |
| A | HOH751 |
| A | HOH765 |
| B | ALA288 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 612 |
| Chain | Residue |
| A | ARG448 |
| A | THR473 |
| A | ASN474 |
| A | GLN475 |
| C | LYS49 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 613 |
| Chain | Residue |
| A | LYS476 |
| A | SER515 |
| A | GLU516 |
| A | LEU517 |
| A | HOH753 |
| A | HOH848 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 614 |
| Chain | Residue |
| A | GLY541 |
| A | GLY543 |
| A | GLU546 |
| A | HOH764 |
| B | ARG284 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 615 |
| Chain | Residue |
| A | GLN547 |
| A | LYS550 |
| A | LEU551 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 616 |
| Chain | Residue |
| A | TYR339 |
| A | GLN340 |
| A | GLY352 |
| A | EDO617 |
| A | HOH748 |
| A | HOH920 |
| site_id | AD8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 617 |
| Chain | Residue |
| A | GLN330 |
| A | EDO616 |
| site_id | AD9 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 618 |
| Chain | Residue |
| A | LYS331 |
| A | GLY333 |
| A | GLN334 |
| A | GLY335 |
| A | ARG356 |
| A | ASP364 |
| A | GLN367 |
| A | HOH744 |
| site_id | AE1 |
| Number of Residues | 9 |
| Details | binding site for residue PGE B 501 |
| Chain | Residue |
| B | HOH739 |
| B | VAL75 |
| B | PHE77 |
| B | ASN81 |
| B | GLY152 |
| B | TYR183 |
| B | THR386 |
| B | TRP410 |
| B | ILE411 |
| site_id | AE2 |
| Number of Residues | 12 |
| Details | binding site for residue PGE B 502 |
| Chain | Residue |
| B | LYS30 |
| B | ILE63 |
| B | LYS64 |
| B | LYS65 |
| B | LYS66 |
| B | ASP67 |
| B | THR403 |
| B | GLU404 |
| B | TRP406 |
| B | GLN407 |
| B | EDO520 |
| D | HOH693 |
| site_id | AE3 |
| Number of Residues | 11 |
| Details | binding site for residue PGE B 503 |
| Chain | Residue |
| B | LYS65 |
| B | LYS66 |
| B | TYR188 |
| B | TYR232 |
| B | THR377 |
| B | GLN407 |
| B | ALA408 |
| B | TRP410 |
| B | EDO507 |
| B | EDO509 |
| B | HOH781 |
| site_id | AE4 |
| Number of Residues | 12 |
| Details | binding site for residue PGE B 504 |
| Chain | Residue |
| A | GLU194 |
| A | HOH961 |
| B | ILE94 |
| B | PRO95 |
| B | PRO97 |
| B | LYS172 |
| B | ILE180 |
| B | TYR181 |
| B | GLN182 |
| B | HOH666 |
| B | HOH772 |
| B | HOH847 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 505 |
| Chain | Residue |
| B | TRP24 |
| B | GLU399 |
| B | TRP402 |
| B | EDO506 |
| B | HOH678 |
| site_id | AE6 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 506 |
| Chain | Residue |
| B | TRP24 |
| B | ARG78 |
| B | GLU399 |
| B | TRP414 |
| B | EDO505 |
| B | HOH634 |
| B | HOH720 |
| B | HOH741 |
| site_id | AE7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 507 |
| Chain | Residue |
| B | LYS66 |
| B | TYR232 |
| B | GLU370 |
| B | GLN373 |
| B | THR377 |
| B | PGE503 |
| B | EDO508 |
| site_id | AE8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 508 |
| Chain | Residue |
| B | TRP239 |
| B | LYS374 |
| B | GLU378 |
| B | EDO507 |
| site_id | AE9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 509 |
| Chain | Residue |
| B | LYS65 |
| B | VAL108 |
| B | ASP110 |
| B | ASP186 |
| B | TYR232 |
| B | PGE503 |
| site_id | AF1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 510 |
| Chain | Residue |
| B | GLU328 |
| B | ILE329 |
| B | GLN330 |
| B | PRO392 |
| B | PRO421 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 511 |
| Chain | Residue |
| B | GLN334 |
| B | GLY335 |
| B | HIS361 |
| B | HOH652 |
| B | HOH733 |
| B | HOH779 |
| site_id | AF3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 512 |
| Chain | Residue |
| B | GLU6 |
| B | VAL8 |
| B | VAL118 |
| B | SER162 |
| B | HOH619 |
| site_id | AF4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 513 |
| Chain | Residue |
| B | PRO1 |
| B | SER3 |
| B | PRO119 |
| B | ARG125 |
| B | ASN147 |
| B | HOH657 |
| B | HOH770 |
| site_id | AF5 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 514 |
| Chain | Residue |
| B | SER3 |
| B | SER117 |
| site_id | AF6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 515 |
| Chain | Residue |
| A | GLU169 |
| B | GLU42 |
| B | LYS49 |
| site_id | AF7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 516 |
| Chain | Residue |
| B | ASN81 |
| B | LYS154 |
| B | MET184 |
| B | HOH739 |
| site_id | AF8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 517 |
| Chain | Residue |
| B | ILE94 |
| B | PRO157 |
| B | TYR181 |
| B | GLN182 |
| B | TYR183 |
| B | MET184 |
| site_id | AF9 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 518 |
| Chain | Residue |
| B | LYS126 |
| site_id | AG1 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 519 |
| Chain | Residue |
| B | PHE416 |
| B | ASN418 |
| B | HOH601 |
| B | HOH740 |
| B | HOH827 |
| C | GLU28 |
| C | GLU29 |
| C | EDO618 |
| site_id | AG2 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 520 |
| Chain | Residue |
| B | ARG358 |
| B | LYS366 |
| B | GLU404 |
| B | TYR405 |
| B | PGE502 |
| B | HOH756 |
| D | GLU300 |
| D | HOH775 |
| site_id | AG3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 521 |
| Chain | Residue |
| B | THR27 |
| B | THR400 |
| B | TRP401 |
| B | GLU404 |
| B | EDO523 |
| B | HOH631 |
| site_id | AG4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 522 |
| Chain | Residue |
| B | THR240 |
| B | VAL241 |
| B | GLN242 |
| B | TYR339 |
| B | GLY352 |
| B | LYS353 |
| B | HOH712 |
| site_id | AG5 |
| Number of Residues | 9 |
| Details | binding site for residue EDO B 523 |
| Chain | Residue |
| B | PRO25 |
| B | LEU26 |
| B | THR27 |
| B | LYS30 |
| B | THR403 |
| B | EDO521 |
| B | HOH602 |
| B | HOH631 |
| B | HOH705 |
| site_id | AG6 |
| Number of Residues | 4 |
| Details | binding site for residue MN C 601 |
| Chain | Residue |
| C | ASP443 |
| C | GLU478 |
| C | ASP498 |
| C | ZW2603 |
| site_id | AG7 |
| Number of Residues | 5 |
| Details | binding site for residue MN C 602 |
| Chain | Residue |
| C | ASP443 |
| C | ASP549 |
| C | ZW2603 |
| C | HOH755 |
| C | HOH882 |
| site_id | AG8 |
| Number of Residues | 10 |
| Details | binding site for residue ZW2 C 603 |
| Chain | Residue |
| C | ASP443 |
| C | GLU478 |
| C | ASP498 |
| C | HIS539 |
| C | ASP549 |
| C | MN601 |
| C | MN602 |
| C | EDO622 |
| C | EDO623 |
| C | HOH882 |
| site_id | AG9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 604 |
| Chain | Residue |
| C | ASP121 |
| C | GLU122 |
| C | ASP123 |
| C | EDO605 |
| C | HOH701 |
| site_id | AH1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 605 |
| Chain | Residue |
| C | VAL10 |
| C | LYS11 |
| C | ASP121 |
| C | ASP123 |
| C | EDO604 |
| C | HOH933 |
| site_id | AH2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 606 |
| Chain | Residue |
| C | LYS103 |
| C | VAL106 |
| C | TYR188 |
| C | TYR318 |
| site_id | AH3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 607 |
| Chain | Residue |
| C | TYR183 |
| C | ASP186 |
| C | HOH836 |
| site_id | AH4 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 608 |
| Chain | Residue |
| C | PHE346 |
| C | ASN348 |
| site_id | AH5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 609 |
| Chain | Residue |
| C | THR377 |
| C | ILE380 |
| D | TRP24 |
| D | PRO25 |
| D | GLU399 |
| D | PGE502 |
| site_id | AH6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 610 |
| Chain | Residue |
| C | GLN500 |
| D | TRP266 |
| D | HOH702 |
| site_id | AH7 |
| Number of Residues | 8 |
| Details | binding site for residue EDO C 611 |
| Chain | Residue |
| C | GLY436 |
| C | ALA437 |
| C | GLU438 |
| C | ASN460 |
| C | LYS461 |
| C | HOH717 |
| C | HOH827 |
| D | ALA288 |
| site_id | AH8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 612 |
| Chain | Residue |
| A | GLU248 |
| A | LYS249 |
| A | ASP250 |
| C | PRO14 |
| site_id | AH9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 613 |
| Chain | Residue |
| C | PRO1 |
| C | ILE2 |
| C | GLY213 |
| C | HOH837 |
| site_id | AI1 |
| Number of Residues | 1 |
| Details | binding site for residue EDO C 614 |
| Chain | Residue |
| C | GLU6 |
| site_id | AI2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 615 |
| Chain | Residue |
| C | VAL10 |
| C | LYS11 |
| C | LEU12 |
| C | ASP123 |
| C | TYR127 |
| site_id | AI3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 616 |
| Chain | Residue |
| C | ASP17 |
| C | LYS20 |
| C | PRO55 |
| C | TYR56 |
| C | HOH945 |
| site_id | AI4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 617 |
| Chain | Residue |
| C | ASN54 |
| C | PRO55 |
| C | ASN57 |
| C | ARG143 |
| site_id | AI5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 618 |
| Chain | Residue |
| B | LYS395 |
| B | EDO519 |
| B | HOH723 |
| B | HOH740 |
| C | GLU29 |
| site_id | AI6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 619 |
| Chain | Residue |
| C | SER48 |
| C | LYS49 |
| C | ILE50 |
| C | HOH763 |
| site_id | AI7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 620 |
| Chain | Residue |
| C | ARG78 |
| C | ASN81 |
| C | LYS82 |
| C | HOH704 |
| C | HOH810 |
| C | HOH860 |
| site_id | AI8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 621 |
| Chain | Residue |
| C | TYR115 |
| C | GLY152 |
| C | SER156 |
| C | HOH814 |
| site_id | AI9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 622 |
| Chain | Residue |
| C | GLY444 |
| C | ASN474 |
| C | GLU478 |
| C | ZW2603 |
| C | EDO623 |
| site_id | AJ1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 623 |
| Chain | Residue |
| C | GLU478 |
| C | ASP498 |
| C | SER499 |
| C | ZW2603 |
| C | EDO622 |
| C | HOH838 |
| site_id | AJ2 |
| Number of Residues | 8 |
| Details | binding site for residue EDO C 624 |
| Chain | Residue |
| C | TYR427 |
| C | GLN428 |
| C | LEU525 |
| C | LYS528 |
| C | GLU529 |
| C | VAL531 |
| C | HOH710 |
| C | HOH736 |
| site_id | AJ3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 625 |
| Chain | Residue |
| C | PRO4 |
| C | ARG211 |
| C | TRP212 |
| C | HOH976 |
| site_id | AJ4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 626 |
| Chain | Residue |
| C | GLU89 |
| C | GLN161 |
| C | HOH735 |
| site_id | AJ5 |
| Number of Residues | 11 |
| Details | binding site for residue PGE D 501 |
| Chain | Residue |
| D | LEU74 |
| D | VAL75 |
| D | PHE77 |
| D | ASN81 |
| D | GLY152 |
| D | TYR183 |
| D | MET184 |
| D | THR386 |
| D | TRP410 |
| D | ILE411 |
| D | HOH737 |
| site_id | AJ6 |
| Number of Residues | 10 |
| Details | binding site for residue PGE D 502 |
| Chain | Residue |
| C | EDO609 |
| D | TRP24 |
| D | GLU399 |
| D | THR400 |
| D | TRP401 |
| D | TRP402 |
| D | THR403 |
| D | EDO504 |
| D | HOH692 |
| D | HOH694 |
| site_id | AJ7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 503 |
| Chain | Residue |
| D | ILE63 |
| D | LYS64 |
| D | GLU404 |
| D | TRP406 |
| D | GLN407 |
| site_id | AJ8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 504 |
| Chain | Residue |
| D | ARG78 |
| D | GLU399 |
| D | TRP414 |
| D | PGE502 |
| D | HOH607 |
| D | HOH630 |
| site_id | AJ9 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 505 |
| Chain | Residue |
| D | GLN85 |
| D | ASP86 |
| site_id | AK1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 506 |
| Chain | Residue |
| D | VAL241 |
| D | LEU349 |
| D | LYS350 |
| site_id | AK2 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 507 |
| Chain | Residue |
| D | LYS65 |
| D | VAL108 |
| D | LEU109 |
| D | ASP110 |
| D | ASP186 |
| D | MET230 |
| D | HOH678 |
| site_id | AK3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 508 |
| Chain | Residue |
| D | THR286 |
| D | LYS287 |
| D | GLU291 |
| D | HOH603 |
| site_id | AK4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 509 |
| Chain | Residue |
| D | GLU298 |
| D | LEU301 |
| D | GLU305 |
| D | HOH649 |
| D | HOH684 |
| site_id | AK5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 510 |
| Chain | Residue |
| D | TYR232 |
| D | TRP239 |
| D | LYS374 |
| D | GLU378 |
| site_id | AK6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 511 |
| Chain | Residue |
| D | LYS395 |
| D | GLU396 |
| D | GLU399 |
| D | HOH694 |
| D | HOH748 |
| site_id | AK7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 512 |
| Chain | Residue |
| C | PRO433 |
| D | THR253 |
| D | THR290 |
| D | HOH623 |
| site_id | AK8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 513 |
| Chain | Residue |
| D | TYR183 |
| D | LYS385 |
| D | THR386 |
| D | LYS388 |
| site_id | AK9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 514 |
| Chain | Residue |
| D | GLU328 |
| D | ILE329 |
| D | GLN330 |
| D | LYS390 |
| D | VAL417 |
| D | THR419 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 380 |
| Details | Domain: {"description":"Reverse transcriptase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00405","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 32 |
| Details | Region: {"description":"RT 'primer grip'"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 64 |
| Details | Motif: {"description":"Tryptophan repeat motif"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | Binding site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | Site: {"description":"Essential for RT p66/p51 heterodimerization"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Site: {"description":"Cleavage; by viral protease; partial"} |
| Chain | Residue | Details |
