6AZ3
Cryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin
This is a non-PDB format compatible entry.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| a | 0000463 | biological_process | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
| a | 0003735 | molecular_function | structural constituent of ribosome |
| a | 0005840 | cellular_component | ribosome |
| a | 0006412 | biological_process | translation |
| a | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| a | 1990904 | cellular_component | ribonucleoprotein complex |
| A | 0003735 | molecular_function | structural constituent of ribosome |
| A | 0005840 | cellular_component | ribosome |
| A | 0006412 | biological_process | translation |
| b | 0003735 | molecular_function | structural constituent of ribosome |
| b | 0005840 | cellular_component | ribosome |
| b | 0006412 | biological_process | translation |
| B | 0003735 | molecular_function | structural constituent of ribosome |
| B | 0005840 | cellular_component | ribosome |
| B | 0006412 | biological_process | translation |
| c | 0000463 | biological_process | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
| c | 0003723 | molecular_function | RNA binding |
| c | 0003735 | molecular_function | structural constituent of ribosome |
| C | 0003735 | molecular_function | structural constituent of ribosome |
| C | 0005840 | cellular_component | ribosome |
| C | 0006412 | biological_process | translation |
| C | 1990904 | cellular_component | ribonucleoprotein complex |
| d | 0003723 | molecular_function | RNA binding |
| D | 0003735 | molecular_function | structural constituent of ribosome |
| D | 0005840 | cellular_component | ribosome |
| D | 0006412 | biological_process | translation |
| e | 0003735 | molecular_function | structural constituent of ribosome |
| e | 0005840 | cellular_component | ribosome |
| e | 0006412 | biological_process | translation |
| E | 0002181 | biological_process | cytoplasmic translation |
| E | 0003735 | molecular_function | structural constituent of ribosome |
| E | 0005840 | cellular_component | ribosome |
| E | 0006412 | biological_process | translation |
| E | 0019843 | molecular_function | rRNA binding |
| E | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| E | 1990904 | cellular_component | ribonucleoprotein complex |
| f | 0003735 | molecular_function | structural constituent of ribosome |
| f | 0005840 | cellular_component | ribosome |
| f | 0006412 | biological_process | translation |
| f | 1990904 | cellular_component | ribonucleoprotein complex |
| F | 0003735 | molecular_function | structural constituent of ribosome |
| F | 0005840 | cellular_component | ribosome |
| F | 0006412 | biological_process | translation |
| g | 0003735 | molecular_function | structural constituent of ribosome |
| g | 0005840 | cellular_component | ribosome |
| g | 0006412 | biological_process | translation |
| G | 0003723 | molecular_function | RNA binding |
| G | 0005840 | cellular_component | ribosome |
| G | 0016020 | cellular_component | membrane |
| G | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| G | 1990904 | cellular_component | ribonucleoprotein complex |
| h | 0003735 | molecular_function | structural constituent of ribosome |
| h | 0005840 | cellular_component | ribosome |
| h | 0006412 | biological_process | translation |
| H | 0003735 | molecular_function | structural constituent of ribosome |
| H | 0005840 | cellular_component | ribosome |
| H | 0006412 | biological_process | translation |
| H | 0015934 | cellular_component | large ribosomal subunit |
| i | 0002181 | biological_process | cytoplasmic translation |
| i | 0003735 | molecular_function | structural constituent of ribosome |
| i | 0005840 | cellular_component | ribosome |
| i | 0006412 | biological_process | translation |
| i | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| I | 0003735 | molecular_function | structural constituent of ribosome |
| I | 0005840 | cellular_component | ribosome |
| I | 0006412 | biological_process | translation |
| j | 0003723 | molecular_function | RNA binding |
| j | 0003735 | molecular_function | structural constituent of ribosome |
| j | 0005840 | cellular_component | ribosome |
| j | 0006412 | biological_process | translation |
| j | 0019843 | molecular_function | rRNA binding |
| j | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| j | 0046872 | molecular_function | metal ion binding |
| j | 1990904 | cellular_component | ribonucleoprotein complex |
| J | 0003735 | molecular_function | structural constituent of ribosome |
| J | 0005840 | cellular_component | ribosome |
| J | 0006412 | biological_process | translation |
| J | 1990904 | cellular_component | ribonucleoprotein complex |
| k | 0003735 | molecular_function | structural constituent of ribosome |
| k | 0005840 | cellular_component | ribosome |
| k | 0006412 | biological_process | translation |
| K | 0003723 | molecular_function | RNA binding |
| K | 0003735 | molecular_function | structural constituent of ribosome |
| K | 0005840 | cellular_component | ribosome |
| K | 0006412 | biological_process | translation |
| l | 0003735 | molecular_function | structural constituent of ribosome |
| l | 0005840 | cellular_component | ribosome |
| l | 0006412 | biological_process | translation |
| l | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| l | 1990904 | cellular_component | ribonucleoprotein complex |
| L | 0003735 | molecular_function | structural constituent of ribosome |
| L | 0005737 | cellular_component | cytoplasm |
| L | 0005840 | cellular_component | ribosome |
| L | 0006412 | biological_process | translation |
| L | 0015934 | cellular_component | large ribosomal subunit |
| L | 0043232 | cellular_component | intracellular non-membrane-bounded organelle |
| L | 1990904 | cellular_component | ribonucleoprotein complex |
| m | 0003735 | molecular_function | structural constituent of ribosome |
| m | 0005840 | cellular_component | ribosome |
| m | 0006412 | biological_process | translation |
| M | 0002181 | biological_process | cytoplasmic translation |
| M | 0003723 | molecular_function | RNA binding |
| M | 0003735 | molecular_function | structural constituent of ribosome |
| M | 0005840 | cellular_component | ribosome |
| M | 0006412 | biological_process | translation |
| M | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| M | 0022626 | cellular_component | cytosolic ribosome |
| M | 1990904 | cellular_component | ribonucleoprotein complex |
| n | 0003735 | molecular_function | structural constituent of ribosome |
| n | 0005840 | cellular_component | ribosome |
| n | 0006412 | biological_process | translation |
| N | 0003735 | molecular_function | structural constituent of ribosome |
| N | 0005840 | cellular_component | ribosome |
| N | 0006412 | biological_process | translation |
| N | 1990904 | cellular_component | ribonucleoprotein complex |
| o | 0003735 | molecular_function | structural constituent of ribosome |
| o | 0005840 | cellular_component | ribosome |
| o | 0006412 | biological_process | translation |
| o | 1990904 | cellular_component | ribonucleoprotein complex |
| O | 0000027 | biological_process | ribosomal large subunit assembly |
| O | 0003735 | molecular_function | structural constituent of ribosome |
| O | 0005737 | cellular_component | cytoplasm |
| O | 0005840 | cellular_component | ribosome |
| O | 0006412 | biological_process | translation |
| O | 0008097 | molecular_function | 5S rRNA binding |
| O | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| O | 1990904 | cellular_component | ribonucleoprotein complex |
| p | 0003735 | molecular_function | structural constituent of ribosome |
| p | 0005840 | cellular_component | ribosome |
| p | 0006412 | biological_process | translation |
| p | 1990904 | cellular_component | ribonucleoprotein complex |
| P | 0003735 | molecular_function | structural constituent of ribosome |
| P | 0005840 | cellular_component | ribosome |
| P | 0006412 | biological_process | translation |
| P | 1990904 | cellular_component | ribonucleoprotein complex |
| Q | 0003723 | molecular_function | RNA binding |
| Q | 0003735 | molecular_function | structural constituent of ribosome |
| Q | 0005840 | cellular_component | ribosome |
| Q | 0006412 | biological_process | translation |
| Q | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| R | 0003735 | molecular_function | structural constituent of ribosome |
| R | 0005840 | cellular_component | ribosome |
| R | 0006412 | biological_process | translation |
| R | 1990904 | cellular_component | ribonucleoprotein complex |
| S | 0003735 | molecular_function | structural constituent of ribosome |
| S | 0005840 | cellular_component | ribosome |
| S | 0006412 | biological_process | translation |
| S | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| S | 1990904 | cellular_component | ribonucleoprotein complex |
| T | 0002181 | biological_process | cytoplasmic translation |
| T | 0003735 | molecular_function | structural constituent of ribosome |
| T | 0005840 | cellular_component | ribosome |
| T | 0006412 | biological_process | translation |
| T | 0015934 | cellular_component | large ribosomal subunit |
| T | 0022625 | cellular_component | cytosolic large ribosomal subunit |
| T | 1990904 | cellular_component | ribonucleoprotein complex |
| U | 0003735 | molecular_function | structural constituent of ribosome |
| U | 0005840 | cellular_component | ribosome |
| U | 0006412 | biological_process | translation |
| U | 1990904 | cellular_component | ribonucleoprotein complex |
| V | 0003735 | molecular_function | structural constituent of ribosome |
| V | 0005840 | cellular_component | ribosome |
| V | 0006412 | biological_process | translation |
| V | 0019843 | molecular_function | rRNA binding |
| W | 0003723 | molecular_function | RNA binding |
| W | 0003735 | molecular_function | structural constituent of ribosome |
| W | 0006412 | biological_process | translation |
| W | 0015934 | cellular_component | large ribosomal subunit |
| Y | 0003735 | molecular_function | structural constituent of ribosome |
| Y | 0005840 | cellular_component | ribosome |
| Y | 0006412 | biological_process | translation |
| Z | 0003735 | molecular_function | structural constituent of ribosome |
| Z | 0005840 | cellular_component | ribosome |
| Z | 0006412 | biological_process | translation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | binding site for residue PAR 1 1801 |
| Chain | Residue |
| 1 | U771 |
| P | ARG149 |
| P | ARG157 |
| 1 | G772 |
| 1 | G773 |
| 1 | C804 |
| 1 | U833 |
| 1 | U834 |
| 1 | G835 |
| 1 | A837 |
| P | ARG66 |
| site_id | AC2 |
| Number of Residues | 12 |
| Details | binding site for residue PAR 1 1802 |
| Chain | Residue |
| 1 | OMC695 |
| 1 | A2M697 |
| 1 | A698 |
| 1 | C699 |
| 1 | A700 |
| 1 | G701 |
| 1 | C843 |
| 1 | C844 |
| 1 | OMU845 |
| 1 | HOH2008 |
| C | ARG109 |
| M | ARG204 |
| site_id | AC3 |
| Number of Residues | 9 |
| Details | binding site for residue PAR 1 1803 |
| Chain | Residue |
| 1 | G1022 |
| 1 | G1023 |
| 1 | U1024 |
| 1 | G1163 |
| 1 | C1164 |
| 1 | A1165 |
| P | SER9 |
| P | LYS10 |
| P | SER12 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | binding site for residue PAR 1 1804 |
| Chain | Residue |
| 1 | A470 |
| 1 | G471 |
| 1 | U472 |
| 1 | A473 |
| 1 | G656 |
| 1 | G658 |
| 1 | G659 |
| g | GLY123 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue PAR 1 1805 |
| Chain | Residue |
| 1 | G893 |
| 1 | G894 |
| 1 | G895 |
| 1 | G896 |
| 1 | C900 |
| 1 | C901 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue MG 1 1806 |
| Chain | Residue |
| 1 | G385 |
| C | GLY98 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | binding site for residue MG 1 1808 |
| Chain | Residue |
| 1 | A1460 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue MG 1 1811 |
| Chain | Residue |
| 1 | A692 |
| 1 | U1522 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue MG 1 1812 |
| Chain | Residue |
| 1 | U914 |
| 1 | A944 |
| site_id | AD1 |
| Number of Residues | 1 |
| Details | binding site for residue MG 1 1813 |
| Chain | Residue |
| 1 | A60 |
| site_id | AD2 |
| Number of Residues | 1 |
| Details | binding site for residue MG 1 1814 |
| Chain | Residue |
| 1 | A50 |
| site_id | AD3 |
| Number of Residues | 1 |
| Details | binding site for residue MG 1 1815 |
| Chain | Residue |
| 1 | C1623 |
| site_id | AD4 |
| Number of Residues | 2 |
| Details | binding site for residue MG 1 1816 |
| Chain | Residue |
| 1 | A61 |
| 1 | U360 |
| site_id | AD5 |
| Number of Residues | 3 |
| Details | binding site for residue MG 1 1817 |
| Chain | Residue |
| 1 | G1614 |
| 1 | C1615 |
| 1 | A1616 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue MG 1 1818 |
| Chain | Residue |
| 1 | U1586 |
| 1 | G1587 |
| 2 | U54 |
| site_id | AD7 |
| Number of Residues | 2 |
| Details | binding site for residue MG 1 1819 |
| Chain | Residue |
| 1 | U307 |
| 1 | G309 |
| site_id | AD8 |
| Number of Residues | 2 |
| Details | binding site for residue MG 1 1820 |
| Chain | Residue |
| 1 | U742 |
| 1 | C744 |
| site_id | AD9 |
| Number of Residues | 1 |
| Details | binding site for residue MG 1 1821 |
| Chain | Residue |
| 1 | G676 |
| site_id | AE1 |
| Number of Residues | 1 |
| Details | binding site for residue MG 1 1822 |
| Chain | Residue |
| 1 | G249 |
| site_id | AE2 |
| Number of Residues | 3 |
| Details | binding site for residue MG 1 1823 |
| Chain | Residue |
| 1 | C982 |
| 1 | A984 |
| C | MET59 |
| site_id | AE3 |
| Number of Residues | 1 |
| Details | binding site for residue MG 1 1826 |
| Chain | Residue |
| 1 | G114 |
| site_id | AE4 |
| Number of Residues | 2 |
| Details | binding site for residue MG 2 1701 |
| Chain | Residue |
| 1 | G967 |
| 2 | G1396 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue C 2 1601 |
| Chain | Residue |
| 2 | C1471 |
| 2 | A1496 |
| 2 | G1497 |
| 2 | C1526 |
| site_id | AE6 |
| Number of Residues | 11 |
| Details | binding site for residue PAR 2 1702 |
| Chain | Residue |
| 2 | G406 |
| 2 | C410 |
| 2 | C411 |
| 2 | A413 |
| 2 | G414 |
| 2 | G416 |
| 2 | U672 |
| 2 | U1023 |
| 2 | C1024 |
| 2 | U1025 |
| 2 | PAR1703 |
| site_id | AE7 |
| Number of Residues | 14 |
| Details | binding site for residue PAR 2 1703 |
| Chain | Residue |
| 2 | C763 |
| 2 | G764 |
| 2 | A765 |
| 2 | U1023 |
| 2 | C1024 |
| 2 | PAR1702 |
| 2 | A404 |
| 2 | G406 |
| 2 | C407 |
| 2 | U418 |
| 2 | G419 |
| 2 | U420 |
| 2 | U422 |
| 2 | A423 |
| site_id | AE8 |
| Number of Residues | 7 |
| Details | binding site for residue PAR 2 1704 |
| Chain | Residue |
| 2 | G447 |
| 2 | C481 |
| 2 | G664 |
| 2 | C668 |
| 2 | U1032 |
| 2 | G1033 |
| 2 | HOH1968 |
| site_id | AE9 |
| Number of Residues | 8 |
| Details | binding site for residue PAR 2 1705 |
| Chain | Residue |
| 2 | G519 |
| 2 | U520 |
| 2 | A521 |
| 2 | G551 |
| 2 | C552 |
| 2 | G553 |
| 2 | U556 |
| 2 | G557 |
| site_id | AF1 |
| Number of Residues | 1 |
| Details | binding site for residue MG 2 1706 |
| Chain | Residue |
| 2 | G380 |
| site_id | AF2 |
| Number of Residues | 1 |
| Details | binding site for residue MG 2 1708 |
| Chain | Residue |
| 2 | C1193 |
| site_id | AF3 |
| Number of Residues | 1 |
| Details | binding site for residue MG 2 1709 |
| Chain | Residue |
| 2 | A1226 |
| site_id | AF4 |
| Number of Residues | 1 |
| Details | binding site for residue MG 2 1711 |
| Chain | Residue |
| 2 | G34 |
| site_id | AF5 |
| Number of Residues | 1 |
| Details | binding site for residue MG 5 201 |
| Chain | Residue |
| 5 | A14 |
| site_id | AF6 |
| Number of Residues | 12 |
| Details | binding site for residue PAR 7 201 |
| Chain | Residue |
| 1 | U439 |
| 1 | A449 |
| 1 | G450 |
| 1 | U1488 |
| 1 | U1489 |
| 1 | U1507 |
| 4 | G9 |
| 7 | G9 |
| 7 | C10 |
| 7 | G11 |
| 7 | A12 |
| 7 | HOH301 |
| site_id | AF7 |
| Number of Residues | 2 |
| Details | binding site for residue MG 7 202 |
| Chain | Residue |
| 7 | C105 |
| 7 | A108 |
| site_id | AF8 |
| Number of Residues | 1 |
| Details | binding site for residue MG 7 203 |
| Chain | Residue |
| 1 | A382 |
| site_id | AF9 |
| Number of Residues | 10 |
| Details | binding site for residues A2M 1 1541 and OMG 1 1542 |
| Chain | Residue |
| 1 | U1540 |
| 1 | C1543 |
| 1 | HOH1995 |
| 2 | U595 |
| 2 | G599 |
| 2 | C600 |
| 2 | G601 |
| 2 | A602 |
| 2 | C1422 |
| 2 | HOH1820 |
Functional Information from PROSITE/UniProt
| site_id | PS00049 |
| Number of Residues | 27 |
| Details | RIBOSOMAL_L14 Ribosomal protein L14 signature. AVIIrqrkswrrk.DGtviyFedNagVI |
| Chain | Residue | Details |
| J | ALA78-ILE104 |
| site_id | PS00050 |
| Number of Residues | 16 |
| Details | RIBOSOMAL_L23 Ribosomal protein L23 signature. KKAYIRLSaahdaldT |
| Chain | Residue | Details |
| V | LYS123-THR138 |
| site_id | PS00051 |
| Number of Residues | 17 |
| Details | RIBOSOMAL_L39E Ribosomal protein L39e signature. RTgnrIkwNekrRHWRR |
| Chain | Residue | Details |
| l | ARG30-ARG46 |
| site_id | PS00358 |
| Number of Residues | 17 |
| Details | RIBOSOMAL_L5 Ribosomal protein L5 signature. LeqLCEQtpVlSrARlT |
| Chain | Residue | Details |
| D | LEU39-THR55 |
| site_id | PS00464 |
| Number of Residues | 25 |
| Details | RIBOSOMAL_L22 Ribosomal protein L22 signature. RrrTyRAhGRitpymcspCHVQLfM |
| Chain | Residue | Details |
| T | ARG126-MET150 |
| site_id | PS00467 |
| Number of Residues | 12 |
| Details | RIBOSOMAL_L2 Ribosomal protein L2 signature. PkvRGVArNPvE |
| Chain | Residue | Details |
| A | PRO197-GLU208 |
| site_id | PS00474 |
| Number of Residues | 24 |
| Details | RIBOSOMAL_L3 Ribosomal protein L3 signature. FqqseacDvcSvTkGHGteGvvkR |
| Chain | Residue | Details |
| B | PHE214-ARG237 |
| site_id | PS00634 |
| Number of Residues | 33 |
| Details | RIBOSOMAL_L30 Ribosomal protein L30 signature. ILqlLrLrQifNtVfvkmnkpmenMLraVepYI |
| Chain | Residue | Details |
| c | ILE112-ILE144 |
| site_id | PS00700 |
| Number of Residues | 22 |
| Details | RIBOSOMAL_L6_2 Ribosomal protein L6 signature 2. QmclVkkKdiRkFlDGIYVqtK |
| Chain | Residue | Details |
| E | GLN162-LYS183 |
| site_id | PS00709 |
| Number of Residues | 25 |
| Details | RIBOSOMAL_L30E_1 Ribosomal protein L30e signature 1. SgkyvlGtQqaLTtlRqGrsKlIVI |
| Chain | Residue | Details |
| d | SER22-ILE46 |
| site_id | PS00939 |
| Number of Residues | 27 |
| Details | RIBOSOMAL_L1E Ribosomal protein L1e signature. NlhqKrfAVvSALaASSvpslvmsRGH |
| Chain | Residue | Details |
| C | ASN115-HIS141 |
| site_id | PS00993 |
| Number of Residues | 21 |
| Details | RIBOSOMAL_L30E_2 Ribosomal protein L30e signature 2. DLGTacGKhfrtcvLsVtNvG |
| Chain | Residue | Details |
| d | ASP78-GLY98 |
| site_id | PS01077 |
| Number of Residues | 20 |
| Details | RIBOSOMAL_L37E Ribosomal protein L37e signature. GTtSmGqRhgrt.HilCrRCG |
| Chain | Residue | Details |
| j | GLY4-GLY23 |
| site_id | PS01170 |
| Number of Residues | 19 |
| Details | RIBOSOMAL_L6E Ribosomal protein L6e signature. NgvPIRRidsrYVIATSt.K |
| Chain | Residue | Details |
| F | ASN72-LYS90 |
| site_id | PS01171 |
| Number of Residues | 26 |
| Details | RIBOSOMAL_L21E Ribosomal protein L21e signature. GDyVdvvadsavre.GmpHkyYhGrTG |
| Chain | Residue | Details |
| S | GLY37-GLY62 |
| site_id | PS01172 |
| Number of Residues | 12 |
| Details | RIBOSOMAL_L44E Ribosomal protein L44e signature. KtTKKivLKlqC |
| Chain | Residue | Details |
| p | LYS63-CYS74 |
| site_id | PS01257 |
| Number of Residues | 22 |
| Details | RIBOSOMAL_L10E Ribosomal protein L10e signature. ADRlqtGMRgAFGKPnGvcARV |
| Chain | Residue | Details |
| N | ALA108-VAL129 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 18 |
| Details | ZN_FING: C4-type => ECO:0000255 |
| Chain | Residue | Details |
| j | CYS19-CYS37 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000250 |
| Chain | Residue | Details |
| j | CYS19 | |
| j | CYS22 | |
| j | CYS34 | |
| j | CYS37 |
