1YHQ: Azithromycin

Crystal Structure Of Azithromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui. Determined by X-ray diffraction at 2.4 Å resolution. Released 26 Apr 2005.

Method
X-ray diffraction
Resolution
2.4 Å
Organism
Haloarcula marismortui
Chains
31
Atoms
99,116
Mol. weight
1489.81 kDa
Ligands
ZIT, MG, SR, CD
Released
26 Apr 2005

Explore 1YHQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YHQ contains 191 α-helices and 196 β-strands across 29 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 1: 3 helices, 3 β-strands

ElementResiduesLengthSheet
α-helix5-84
β-strand16-1839
β-strand25-2849
β-strand33-3429
α-helix45-462
α-helix49-513
Chain 2: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix5-1713
α-helix20-223
α-helix23-286
Chain 3: 5 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand2-4317
β-strand6-11618
β-strand16-24918
α-helix26-305
α-helix35-439
α-helix50-534
α-helix631
β-strand64119
α-helix651
β-strand67-71518
β-strand77-78218
β-strand84119
β-strand89-91317
Chain A: 11 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix5-106
α-helix14-163
α-helix20-223
α-helix28-314
β-strand39-48104
β-strand53-6084
β-strand65-6844
β-strand7115
β-strand7513
β-strand79-8134
β-strand8216
β-strand93-9536
α-helix96-983
α-helix1001
β-strand104-10636
β-strand10817
β-strand11817
β-strand126-13056
β-strand136-13946
β-strand145-14846
β-strand153-15646
β-strand15915
α-helix164-1663
α-helix172-1798
α-helix191-1933
α-helix196-1983
β-strand214-21528
α-helix219-2202
β-strand227-22828
Chain B: 11 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand37-38210
β-strand41-541411
β-strand66-751011
β-strand79-901210
β-strand93-101910
α-helix109-1113
α-helix121-13414
β-strand137-145910
α-helix148-1503
α-helix159-1602
β-strand161-167710
α-helix171-18414
β-strand187-188210
α-helix190-1934
β-strand199-205711
α-helix206-2072
β-strand208-212512
α-helix214-2185
α-helix220-2234
α-helix225-2295
β-strand255-258412
β-strand261-2751511
α-helix279-2802
β-strand284113
β-strand288113
β-strand292-298711
β-strand308-313611
β-strand327-330411
Chain C: 16 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand2-6514
β-strand12-17614
α-helix18-192
α-helix20-234
α-helix25-262
α-helix28-4114
α-helix43-453
β-strand59115
β-strand72-73215
β-strand76-77215
α-helix86-883
α-helix104-11714
α-helix121-1277
β-strand138-140314
α-helix142-1465
α-helix150-15910
α-helix164-1685
β-strand173-174216
α-helix178-1825
β-strand186-187216
β-strand193-196414
α-helix202-2054
β-strand211-214414
α-helix220-2234
α-helix225-2273
β-strand233-236414
α-helix237-2437
Chain D: 7 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand17-261020
α-helix38-458
β-strand50-52320
β-strand58121
β-strand62121
β-strand70-75620
α-helix78-8710
α-helix88-903
β-strand98120
β-strand104-106320
β-strand129-135720
α-helix139-1424
α-helix150-1523
α-helix153-1553
α-helix159-1679
Chain E: 6 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand2-6522
α-helix7-82
β-strand12-16523
β-strand19-24623
β-strand27-32623
β-strand39-43522
β-strand46-50522
α-helix56-7621
β-strand80-87824
β-strand94-97425
β-strand101-105525
α-helix107-1093
α-helix1131
β-strand114-117425
α-helix118-1192
β-strand123-127524
β-strand130-135624
α-helix138-15013
β-strand165-170624

21 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
23S Ribosomal RNA0RNA2922Haloarcula marismortui
5S Ribosomal RNA9RNA122Haloarcula marismortui
50S ribosomal protein L2PAprotein240Haloarcula marismortuiP20276 (AlphaFold model)
50S ribosomal protein L3PBprotein338Haloarcula marismortuiP20279 (AlphaFold model)
50S ribosomal protein L4ECprotein246Haloarcula marismortuiP12735 (AlphaFold model)
50S ribosomal protein L5PDprotein177Haloarcula marismortuiP14124 (AlphaFold model)
50S ribosomal protein L6PEprotein178Haloarcula marismortuiP14135
50S ribosomal protein L7AEFprotein120Haloarcula marismortuiP12743
Acidic ribosomal protein P0 homologGprotein348Haloarcula marismortuiP15825
50S ribosomal protein L10EHprotein177Haloarcula marismortuiP60617
50S ribosomal protein L11PIprotein162Haloarcula marismortuiP14122
50S ribosomal protein L13PJprotein145Haloarcula marismortuiP29198

19 more molecules are not listed.

Sequence of entity 1 (0), FASTA
>1YHQ_1 23S Ribosomal RNA (chains 0)
GUUGGCUACUAUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAA
GCUGCGAUAAGCUGUGGGGAGCCGCACGGAGGCGAAGAACCACAGAUUUCCGAAUGAGAA
UCUCUCUAACAAUUGCUUCGCGCAAUGAGGAACCCCGAGAACUGAAACAUCUCAGUAUCG
GGAGGAACAGAAAACGCAACGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCC
AAACCGAAGCCCUCACGGGCAAUGUGGUGUCAGGGCUACCUCUCAUCAGCCGACCGUCUU
CACGAAGUCUCUUGGAAUAGAGCGUGAUACAGGGUGACAACCCCGUACUGAAGACCAGUA
CGCUGUGCGGUAGUGCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAACGCAGGCAU
CGACUGCGAAGGCUAAACACAACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGC
UGCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCGAUCGAGCGA
CAGGGCAUACAAGGUCCCUUGACGAAUGACCGAGACGCGAGUCUCCAGUAAGACUCACGG
GAAGCCGAUGUUCUGUCGUACGUUUUGAAAAACGAGCCAGGGAGUGUGUCUGUAUGGCAA
GUCUAACCGGAGUAUCCGGGGAGGCACAGGGAAACCGACAUGGCCGCAGGGCUUUGCCCG
AGGGCCGCCGUCUUCAAGGGCGGGGAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUA
CGCAUGGACAAGAUGAAGCGUGCCGAAAGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCU
ACAAUACCCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCU
GGUUCCAAUCGAAACAUGUCGAAGCAUGACCUCCGCCGAGGUAGUCUGUGAGGUAGAGCG
ACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACA
GACGCUGUUUGACGCGGGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAAC
AACCCAGAGAUAGGUUAAGGUCCCCAAGUGUGGAUUAAGUGUAAUCCUCUGAAGGUGGUC
UCGAGCCCUAGACAGCCGGGAGGUGAGCUUAGAAGCAGCUACCCUCUAAGAAAAGCGUAA
CAGCUUACCGGCCGAGGUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAG
ACCUGUCCGUACCACUCAUACUGGUAAUCGAGUAGAUUGGCGCUCUAAUUGGAUGGAAGC
AGGGGCGAGAGCUCCUGUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAU
AGUCGGGUGAGAACCCCGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCU
GAGGGUUAGCCGGUCCUAAGUCUCACCGCAACUCGACUGAGACGAAAUGGGAAACAGGUU
AAUAUUCCUGUGCCAUCAUGCAGUGAAAGUUGACGCCCUGGGGUCGAUCACGCCGGGCAU
UCGCCCGGUCGAACCGUCCAACUCCGUGGAAGCCGUAAUGGCAGGAAGCGGACGAACGGC
GGCAUAGGGAAACGUGAUUCAACCUGGGGCCCAUGAAAAGACGAGCAUGAUGUCCGUACC
GAGAACCGACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGU
UAGGGAAUUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGGAACGG
AGCAGGUCGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAU
CCGCAAGGACUCGUACGGUCACUGAAUCCUGCCCAGUGCAGGUAUCUGAACACCUCGUAC
AAGAGGACGAAGGACCUGUCAACGGCGGGGGUAACUAUGACCCUCUUAAGGUAGCGUAGU
ACCUUGCCGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAAC
GUUGGGCCCGGUGAACUGUACAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCAA
AGACCCUAUGGAGCUUUACUGCAGGCUGUCGCUGAGACGUGGUCGCCGAUGUGCAGCAUA
GGUAGGAGUCGUUACAGAGGUACCCGCGCUAGCGGGCCACCCAGACAACAGUGAAAUACU
ACCCGUCGGUGACUGCGACUCUCACUCCGGGAGGAGGACACCGAUAGCCGGGCAGUUUGA
CUGGGGCGGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGUCAUCUCAGCCGGGAC
AGAGACCCGGCGAAGAGUGCAAGAGCAAAAGAUGACUUGACAGUGUUCUUCCCAACGAGG
AACGCUGACGCGAAAGCGUGGUCUAGCGAACCAAUUAGCCUGCUUGAUGCGGGCAAUUGA
UGACAGAAAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCACAUAUCGACCG
AGUGGCUUGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGGCAAGGG
UGAGGUUGUUCGCCUAUUAAAGGAGGUCGUGAGCUGGGUUUAGACCGUCGUGAGACAGGU
CGGCUGCUAUCUACUGGGUGUGUAAUGGUGUCUGACAAGAACGACCGUAUAGUACGAGAG
GAACUACGGUUGGUGGCCACUGGUGUACCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCC
ACGCCACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACA
CCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAA
CGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCA
Sequence of entity 2 (9), FASTA
>1YHQ_2 5S Ribosomal RNA (chains 9)
UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCC
CACCAGCGUUCCAGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCA
CC
Sequence of entity 3 (A), FASTA
>1YHQ_3 50S ribosomal protein L2P (chains A)
MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVE
FEDGDRRLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFA
RASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKM
KARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE
Sequence of entity 4 (B), FASTA
>1YHQ_4 50S ribosomal protein L3P (chains B)
MPQPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPGVQGFAGYKAGMTHVVLVNDEPN
SPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDH
DPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHAL
DIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNL
GPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDEPTVDGGFVNYGEVDGPYTLVKG
SVPGPDKRLVRFRPAVRPNDQPRLDPEVRYVSNESNQG
Sequence of entity 5 (C), FASTA
>1YHQ_5 50S ribosomal protein L4E (chains C)
MQATIYDLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAES
FGSGRGQAHVPKLDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATAD
ADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAGQGS
ARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESAL
AEVAER
Sequence of entity 6 (D), FASTA
>1YHQ_6 50S ribosomal protein L5P (chains D)
MSSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVG
EFDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGVEEHTEFPSQEY
DPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVSE
Sequence of entity 7 (E), FASTA
>1YHQ_7 50S ribosomal protein L6P (chains E)
MPRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTM
STIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIH
GDTDVEIDGEELTVSGPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKPNRGDA
Sequence of entity 8 (F), FASTA
>1YHQ_8 50S ribosomal protein L7AE (chains F)
MPVYVDFDVPADLEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEI
VMHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVTDAGEADADVEDIADKVEELR
Sequence of entity 9 (G), FASTA
>1YHQ_9 ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG (chains G)
MSAESERKTETIPEWKQEEVDAIVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELR
VSRNTLLERALDDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVA
PNDIVIPEGDTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLN
ELGIEPKEVGLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATT
APTMLQSDRGNAKSLALQAAIEDPEVVPDLVSKADAQVRALASQIDDEEALPEELQGVEA
DVATEEPTDDQDDDTASEDDADADDAAEEADDDDDDDEDAGDALGAMF
Sequence of entity 10 (H), FASTA
>1YHQ_10 50S RIBOSOMAL PROTEIN L10E (chains H)
MSDKPASMYRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQL
RHGSLEASRLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAF
GKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVERGEELLIA
Sequence of entity 11 (I), FASTA
>1YHQ_11 50S RIBOSOMAL PROTEIN L11P (chains I)
MAGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAFDGTEVPVTVKYDDDG
SFEIEVGVPPTAELIKDEAGFETGSGEPQEDFVADLSVDQVKQIAEQKHPDLLSYDLTNA
AKEVVGTCTSLGVTIEGENPREFKERIDAGEYDDVFAAEAQA
Sequence of entity 12 (J), FASTA
>1YHQ_12 50S ribosomal protein L13P (chains J)
MSVAEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKR
VDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTS
LDRLSNIKFVTLGEISETLGANKTW

Ligands and cofactors

IDNameFormulaCopies
ZITAzithromycinC38 H72 N2 O121
MGMagnesium ionMg93
SRStrontium ionSr108
CDCadmium ionCd5

Water and common crystallization additives (K, NA, CL) are not listed.

Primary citation

Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Tu, D., Blaha, G., Moore, P.B. et al. Cell (2005) 121:257-270. DOI 10.1016/j.cell.2005.02.005 · PubMed

Other PDB entries of the same protein (UniProt P20276 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 1YHQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.