4IO9: Compound 4d
Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans. Determined by X-ray diffraction at 3.2 Å resolution. Released 6 Mar 2013.
- Method
- X-ray diffraction
- Resolution
- 3.2 Å
- Organism
- Deinococcus radiodurans
- Chains
- 30
- Atoms
- 83,875
- Mol. weight
- 1365.95 kDa
- Ligands
- 1F2, MG
- Released
- 6 Mar 2013
Explore 4IO9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4IO9 contains 93 α-helices and 182 β-strands across 25 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 4: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 10 |
| β-strand | 15-16 | 2 | 11 |
| β-strand | 25-26 | 2 | 11 |
| α-helix | 30-32 | 3 | |
| β-strand | 34-35 | 2 | 10 |
Chain A: 7 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 37 | 1 | 1 |
| β-strand | 44 | 1 | 2 |
| β-strand | 49 | 1 | 2 |
| β-strand | 62 | 1 | 1 |
| α-helix | 63-64 | 2 | |
| α-helix | 70-72 | 3 | |
| β-strand | 73 | 1 | 3 |
| β-strand | 76-83 | 8 | 4 |
| β-strand | 92-97 | 6 | 4 |
| β-strand | 102-106 | 5 | 4 |
| α-helix | 107 | 1 | |
| β-strand | 108 | 1 | 5 |
| β-strand | 116-118 | 3 | 4 |
| β-strand | 119 | 1 | 3 |
| β-strand | 130 | 1 | 3 |
| α-helix | 137 | 1 | |
| β-strand | 141-143 | 3 | 3 |
| β-strand | 145 | 1 | 6 |
| β-strand | 155 | 1 | 6 |
| β-strand | 163-168 | 6 | 3 |
| β-strand | 172-176 | 5 | 3 |
| β-strand | 182-186 | 5 | 3 |
| β-strand | 192-193 | 2 | 3 |
| β-strand | 196 | 1 | 5 |
| α-helix | 212-214 | 3 | |
| α-helix | 223-225 | 3 | |
| α-helix | 262-264 | 3 | |
| β-strand | 267 | 1 | 3 |
Chain B: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-16 | 14 | 7 |
| β-strand | 19-27 | 9 | 7 |
| β-strand | 33-37 | 5 | 8 |
| β-strand | 46-50 | 5 | 8 |
| α-helix | 61-70 | 10 | |
| β-strand | 78-82 | 5 | 8 |
| β-strand | 101-107 | 7 | 7 |
| α-helix | 108-110 | 3 | |
| β-strand | 113-114 | 2 | 9 |
| α-helix | 116-120 | 5 | |
| β-strand | 158-159 | 2 | 9 |
| β-strand | 164-176 | 13 | 7 |
| β-strand | 181-185 | 5 | 7 |
| β-strand | 195-200 | 6 | 7 |
Chain C: 6 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-18 | 2 | |
| α-helix | 24-38 | 15 | |
| α-helix | 97-112 | 16 | |
| β-strand | 116-117 | 2 | 12 |
| α-helix | 131-139 | 9 | |
| β-strand | 148-150 | 3 | 12 |
| α-helix | 155-159 | 5 | |
| β-strand | 167-169 | 3 | 12 |
| α-helix | 177-182 | 6 | |
| β-strand | 185-187 | 3 | 12 |
Chain D: 7 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 13-19 | 7 | |
| β-strand | 31-38 | 8 | 13 |
| β-strand | 41 | 1 | 14 |
| β-strand | 44 | 1 | 14 |
| α-helix | 49-60 | 12 | |
| α-helix | 64-65 | 2 | |
| β-strand | 66-68 | 3 | 13 |
| β-strand | 86-91 | 6 | 13 |
| α-helix | 94-101 | 8 | |
| α-helix | 102-107 | 6 | |
| β-strand | 117 | 1 | 15 |
| β-strand | 123 | 1 | 16 |
| β-strand | 127 | 1 | 16 |
| β-strand | 128-132 | 5 | 13 |
| β-strand | 152-158 | 7 | 13 |
| α-helix | 163-174 | 12 | |
| β-strand | 177 | 1 | 15 |
Chain E: 3 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9 | 1 | 17 |
| β-strand | 16-18 | 3 | 18 |
| β-strand | 23 | 1 | 19 |
| β-strand | 25-27 | 3 | 18 |
| β-strand | 32-33 | 2 | 18 |
| β-strand | 36 | 1 | 19 |
| β-strand | 42-46 | 5 | 17 |
| β-strand | 49-53 | 5 | 17 |
| α-helix | 60-80 | 21 | |
| β-strand | 83-90 | 8 | 20 |
| β-strand | 95-99 | 5 | 21 |
| β-strand | 102-106 | 5 | 21 |
| β-strand | 113-115 | 3 | 21 |
| β-strand | 122-124 | 3 | 20 |
| β-strand | 130-135 | 6 | 20 |
| α-helix | 138-150 | 13 | |
| α-helix | 153-155 | 3 | |
| β-strand | 161-163 | 3 | 20 |
Chain F: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 75-81 | 7 | |
| β-strand | 97-98 | 2 | 22 |
| α-helix | 101-104 | 4 | |
| α-helix | 105-108 | 4 | |
| α-helix | 121-128 | 8 | |
| α-helix | 130-134 | 5 | |
| β-strand | 136-137 | 2 | 22 |
| α-helix | 138 | 1 | |
Chain G: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 41-45 | 5 | 23 |
| β-strand | 50 | 1 | 24 |
| α-helix | 51-63 | 13 | |
| β-strand | 79-83 | 5 | 23 |
| α-helix | 85-87 | 3 | |
| β-strand | 89 | 1 | 24 |
| β-strand | 99-101 | 3 | 25 |
| β-strand | 113-115 | 3 | 25 |
| α-helix | 123-131 | 9 | |
| α-helix | 132-134 | 3 | |
| α-helix | 139-143 | 5 | |
| α-helix | 144-146 | 3 | |
| β-strand | 149-150 | 2 | 23 |
| α-helix | 158-160 | 3 | |
| β-strand | 166 | 1 | 23 |
17 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 23S ribosomal RNA | X | RNA | 2880 | Deinococcus radiodurans | |
| 5S ribosomal RNA | Y | RNA | 123 | Deinococcus radiodurans | |
| 50S ribosomal protein L2 | A | protein | 274 | Deinococcus radiodurans | Q9RXJ9 (AlphaFold model) |
| 50S ribosomal protein L3 | B | protein | 211 | Deinococcus radiodurans | Q9RXK2 (AlphaFold model) |
| 50S ribosomal protein L4 | C | protein | 205 | Deinococcus radiodurans | Q9RXK1 (AlphaFold model) |
| 50S ribosomal protein L5 | D | protein | 180 | Deinococcus radiodurans | Q9RXJ0 (AlphaFold model) |
| 50S ribosomal protein L6 | E | protein | 185 | Deinococcus radiodurans | Q9RSL3 |
| 50S ribosomal protein L11 | F | protein | 144 | Deinococcus radiodurans | Q9RSS7 |
| 50S ribosomal protein L13 | G | protein | 174 | Deinococcus radiodurans | Q9RXY1 |
| 50S ribosomal protein L14 | H | protein | 134 | Deinococcus radiodurans | Q9RXJ2 |
| 50S ribosomal protein L15 | I | protein | 156 | Deinococcus radiodurans | Q9RSK9 |
| 50S ribosomal protein L16 | J | protein | 141 | Deinococcus radiodurans | Q9RXJ5 |
18 more molecules are not listed.
Sequence of entity 1 (X), FASTA
>4IO9_1 23S ribosomal RNA (chains X)
GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGA
UUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGG
GGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUC
AGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAU
CAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCC
CUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGA
GCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGC
GCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGG
AAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAG
CAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAG
ACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGG
CGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAA
CCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUU
GUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUU
GAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUA
CCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCU
GCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUA
AAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGA
AGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAA
UGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUG
GUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA
GUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACA
AGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAAC
GGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGG
ACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAU
CGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGA
AGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUAC
CGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUU
AAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGG
GGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAA
CAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAA
GCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAA
AUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCA
ACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGA
AAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGA
UAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCAC
CCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUA
GUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGA
CGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACAC
GUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCG
AUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCG
GCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCA
AGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGAC
AGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAG
AGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGU
AGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUG
AGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGC
GUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC
Sequence of entity 2 (Y), FASTA
>4IO9_2 5S ribosomal RNA (chains Y)
ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAA
ACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGG
GUU
Sequence of entity 3 (A), FASTA
>4IO9_3 50S ribosomal protein L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK
Sequence of entity 4 (B), FASTA
>4IO9_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASAAKGGK
Sequence of entity 5 (C), FASTA
>4IO9_5 50S ribosomal protein L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ
Sequence of entity 6 (D), FASTA
>4IO9_6 50S ribosomal protein L5 (chains D)
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALI
TLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPN
AFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ
Sequence of entity 7 (E), FASTA
>4IO9_7 50S ribosomal protein L6 (chains E)
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK
HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG
VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATG
GKGKK
Sequence of entity 8 (F), FASTA
>4IO9_8 50S ribosomal protein L11 (chains F)
MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIY
ADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSV
EAAANTVAGTARSMGVTVEGGPNA
Sequence of entity 9 (G), FASTA
>4IO9_9 50S ribosomal protein L13 (chains G)
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIAS
RIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALS
KHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK
Sequence of entity 10 (H), FASTA
>4IO9_10 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL
Sequence of entity 11 (I), FASTA
>4IO9_11 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE
Sequence of entity 12 (J), FASTA
>4IO9_12 50S ribosomal protein L16 (chains J)
MLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRR
GGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRL
AGHKLPIQTKMVKREVYDEAQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 1F2 | (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexam… | C41 H64 N4 O11 | 1 |
| MG | Magnesium ion | Mg | 35 |
Primary citation
Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates. Magee, T.V., Han, S., McCurdy, S.P. et al. Bioorg Med Chem Lett (2013) 23:1727-1731. DOI 10.1016/j.bmcl.2013.01.067 · PubMed
Other PDB entries of the same protein (UniProt Q9RXJ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5DM6 2.9 Å, Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans
- 2ZJR 2.91 Å, Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans
- 5DM7 3.0 Å, Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex…
- 1NKW 3.1 Å, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans
- 4IOA 3.2 Å, Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus…
- 7A0S 3.22 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin I
- 3PIO 3.25 Å, Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in…
- 1NWY 3.3 Å, Complex of the large ribosomal subunit from deinococcus radiodurans with azithromycin
- 2ZJQ 3.3 Å, Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans…
- 3CF5 3.3 Å, Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus…
- 7A0R 3.3 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin I
- 7A18 3.4 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV
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