3DLL: 50S ribosomal protein L2
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning. Determined by X-ray diffraction at 3.5 Å resolution. Released 16 Sept 2008.
- Method
- X-ray diffraction
- Resolution
- 3.5 Å
- Organism
- Deinococcus radiodurans
- Chains
- 30
- Atoms
- 83,657
- Mol. weight
- 1365.76 kDa
- Ligands
- ZLD, ZN, MG
- Released
- 16 Sept 2008
Explore 3DLL in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3DLL contains 79 α-helices and 175 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: 0 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 14 |
| β-strand | 16 | 1 | 15 |
| β-strand | 19 | 1 | 16 |
| β-strand | 22 | 1 | 16 |
| β-strand | 25 | 1 | 15 |
| β-strand | 34-35 | 2 | 14 |
Chain A: 1 helix, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 37-38 | 2 | 1 |
| β-strand | 61-62 | 2 | 1 |
| β-strand | 77 | 1 | 2 |
| β-strand | 78 | 1 | 3 |
| β-strand | 81 | 1 | 4 |
| β-strand | 93-95 | 3 | 4 |
| β-strand | 97 | 1 | 2 |
| β-strand | 103-105 | 3 | 4 |
| β-strand | 116 | 1 | 3 |
| β-strand | 131 | 1 | 5 |
| α-helix | 137 | 1 | |
| β-strand | 142-143 | 2 | 6 |
| β-strand | 146 | 1 | 7 |
| β-strand | 153 | 1 | 7 |
| β-strand | 163 | 1 | 6 |
| β-strand | 164 | 1 | 8 |
| β-strand | 168-169 | 2 | 9 |
| β-strand | 172-173 | 2 | 9 |
| β-strand | 175-177 | 3 | 8 |
| β-strand | 181-183 | 3 | 8 |
| β-strand | 186 | 1 | 9 |
| β-strand | 191 | 1 | 5 |
| β-strand | 192-193 | 2 | 6 |
Chain B: 4 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 10 |
| β-strand | 12-16 | 5 | 11 |
| β-strand | 19-23 | 5 | 11 |
| β-strand | 26-28 | 3 | 10 |
| β-strand | 33 | 1 | 12 |
| β-strand | 48-51 | 4 | 12 |
| α-helix | 56-58 | 3 | |
| α-helix | 61-68 | 8 | |
| β-strand | 77-80 | 4 | 12 |
| α-helix | 97 | 1 | |
| β-strand | 101-107 | 7 | 10 |
| β-strand | 110-114 | 5 | 13 |
| α-helix | 116-119 | 4 | |
| β-strand | 158-161 | 4 | 13 |
| β-strand | 164-176 | 13 | 10 |
| β-strand | 181-184 | 4 | 10 |
| β-strand | 185 | 1 | 11 |
| β-strand | 194-200 | 7 | 10 |
Chain C: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-38 | 15 | |
| β-strand | 41 | 1 | 17 |
| β-strand | 89 | 1 | 17 |
| α-helix | 97-111 | 15 | |
| β-strand | 118 | 1 | 18 |
| α-helix | 123-125 | 3 | |
| α-helix | 131-139 | 9 | |
| β-strand | 150-151 | 2 | 19 |
| β-strand | 169-170 | 2 | 19 |
| α-helix | 177-182 | 6 | |
| β-strand | 187 | 1 | 19 |
| β-strand | 188 | 1 | 18 |
Chain D: 6 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-19 | 7 | |
| β-strand | 33-36 | 4 | 20 |
| α-helix | 51-60 | 10 | |
| β-strand | 66-68 | 3 | 21 |
| β-strand | 86-88 | 3 | 21 |
| β-strand | 90-92 | 3 | 20 |
| α-helix | 93-99 | 7 | |
| α-helix | 101 | 1 | |
| α-helix | 102-107 | 6 | |
| β-strand | 128-130 | 3 | 20 |
| β-strand | 154-157 | 4 | 20 |
| α-helix | 163-171 | 9 | |
Chain E: 3 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-9 | 2 | 22 |
| β-strand | 16 | 1 | 23 |
| β-strand | 27 | 1 | 23 |
| β-strand | 42-45 | 4 | 22 |
| β-strand | 50-53 | 4 | 22 |
| α-helix | 60-81 | 22 | |
| β-strand | 83 | 1 | 24 |
| β-strand | 86-90 | 5 | 25 |
| β-strand | 96 | 1 | 26 |
| β-strand | 105 | 1 | 26 |
| β-strand | 124 | 1 | 25 |
| β-strand | 130-132 | 3 | 25 |
| β-strand | 135 | 1 | 24 |
| α-helix | 138-150 | 13 | |
| α-helix | 153-155 | 3 | |
| β-strand | 161-163 | 3 | 25 |
Chain F: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 75-78 | 4 | |
| α-helix | 105-111 | 7 | |
| α-helix | 126-136 | 11 | |
Chain G: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 42-47 | 6 | 27 |
| α-helix | 51-61 | 11 | |
| β-strand | 80-87 | 8 | 27 |
| β-strand | 99-101 | 3 | 28 |
| β-strand | 113-115 | 3 | 28 |
| α-helix | 123-131 | 9 | |
| α-helix | 132-134 | 3 | |
| α-helix | 139-144 | 6 | |
| α-helix | 145-147 | 3 | |
| β-strand | 148-151 | 4 | 27 |
| β-strand | 166 | 1 | 27 |
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 |
|---|
| rRNA-23S ribosomal RNA | X | RNA | 2880 | Deinococcus radiodurans | |
| rRNA-5S ribosomal RNA | Z | 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 | 142 | Deinococcus radiodurans | Q9RXJ5 |
18 more molecules are not listed.
Sequence of entity 1 (X), FASTA
>3DLL_1 rRNA-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 (Z), FASTA
>3DLL_2 rRNA-5S ribosomal RNA (chains Z)
ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAA
ACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGG
GUU
Sequence of entity 3 (A), FASTA
>3DLL_3 50S ribosomal protein L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK
Sequence of entity 4 (B), FASTA
>3DLL_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASAAKGGK
Sequence of entity 5 (C), FASTA
>3DLL_5 50S ribosomal protein L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ
Sequence of entity 6 (D), FASTA
>3DLL_6 50S ribosomal protein L5 (chains D)
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALI
TLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPN
AFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ
Sequence of entity 7 (E), FASTA
>3DLL_7 50S ribosomal protein L6 (chains E)
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK
HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG
VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATG
GKGKK
Sequence of entity 8 (F), FASTA
>3DLL_8 50S ribosomal protein L11 (chains F)
MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIY
ADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSV
EAAANTVAGTARSMGVTVEGGPNA
Sequence of entity 9 (G), FASTA
>3DLL_9 50S ribosomal protein L13 (chains G)
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIAS
RIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALS
KHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK
Sequence of entity 10 (H), FASTA
>3DLL_10 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL
Sequence of entity 11 (I), FASTA
>3DLL_11 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE
Sequence of entity 12 (J), FASTA
>3DLL_12 50S ribosomal protein L16 (chains J)
MMLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFR
RGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFR
LAGHKLPIQTKMVKREVYDEAQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZLD | N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}a… | C16 H20 F N3 O4 | 1 |
| ZN | Zinc ion | Zn | 2 |
| MG | Magnesium ion | Mg | 35 |
Primary citation
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning. Wilson, D.N., Schluenzen, F., Harms, J.M. et al. Proc Natl Acad Sci U S A (2008) 105:13339-13344. DOI 10.1073/pnas.0804276105 · 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
- 4IO9 3.2 Å, Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus…
- 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
Browse structure collections
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