3PIP: 50S ribosomal protein L2
Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit. Determined by X-ray diffraction at 3.45 Å resolution. Released 23 Feb 2011.
- Method
- X-ray diffraction
- Resolution
- 3.45 Å
- Organisms
- Deinococcus radiodurans R1, Deinococcus radiodurans
- Chains
- 30
- Atoms
- 83,963
- Mol. weight
- 1367.64 kDa
- Ligands
- MG, LMA, LC2
- Released
- 23 Feb 2011
Explore 3PIP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3PIP contains 92 α-helices and 189 β-strands across 28 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: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-12 | 2 | 1 |
| β-strand | 25-26 | 2 | 1 |
| β-strand | 37-38 | 2 | 2 |
| α-helix | 41-42 | 2 | |
| β-strand | 50-51 | 2 | 2 |
Chain 2: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-13 | 5 | |
| α-helix | 19-21 | 3 | |
| α-helix | 25-34 | 10 | |
| α-helix | 43-45 | 3 | |
Chain 3: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| β-strand | 24 | 1 | 9 |
| β-strand | 47 | 1 | 9 |
| α-helix | 54-57 | 4 | |
Chain 4: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 17 |
| β-strand | 15-18 | 4 | 18 |
| β-strand | 23-26 | 4 | 18 |
| α-helix | 30-32 | 3 | |
| β-strand | 34 | 1 | 17 |
| β-strand | 35 | 1 | 18 |
Chain A: 2 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 45 | 1 | 3 |
| β-strand | 50 | 1 | 3 |
| β-strand | 78-86 | 9 | 4 |
| β-strand | 91-98 | 8 | 4 |
| β-strand | 103-107 | 5 | 4 |
| β-strand | 109 | 1 | 5 |
| β-strand | 117 | 1 | 4 |
| β-strand | 131-133 | 3 | 6 |
| α-helix | 134-136 | 3 | |
| β-strand | 143-144 | 2 | 6 |
| β-strand | 146 | 1 | 7 |
| β-strand | 156 | 1 | 7 |
| β-strand | 164 | 1 | 6 |
| β-strand | 166-169 | 4 | 8 |
| β-strand | 173-178 | 6 | 8 |
| β-strand | 182-187 | 6 | 8 |
| β-strand | 191-194 | 4 | 6 |
| β-strand | 197 | 1 | 5 |
| α-helix | 263-267 | 5 | |
| β-strand | 268-269 | 2 | 8 |
Chain B: 4 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-12 | 10 | 10 |
| β-strand | 15-16 | 2 | 11 |
| β-strand | 19-20 | 2 | 11 |
| β-strand | 23-27 | 5 | 10 |
| β-strand | 31-32 | 2 | 12 |
| β-strand | 33-35 | 3 | 13 |
| β-strand | 46-50 | 5 | 13 |
| β-strand | 53 | 1 | 14 |
| α-helix | 61-68 | 8 | |
| β-strand | 75 | 1 | 14 |
| β-strand | 78-82 | 5 | 13 |
| β-strand | 89-90 | 2 | 12 |
| α-helix | 92-95 | 4 | |
| β-strand | 101-107 | 7 | 10 |
| β-strand | 110-113 | 4 | 15 |
| α-helix | 116-119 | 4 | |
| β-strand | 125 | 1 | 16 |
| β-strand | 135 | 1 | 16 |
| α-helix | 150-151 | 2 | |
| β-strand | 159-161 | 3 | 15 |
| β-strand | 164-176 | 13 | 10 |
| β-strand | 181-185 | 5 | 10 |
| β-strand | 195-200 | 6 | 10 |
Chain C: 7 helices, 3 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 | 19 |
| α-helix | 123-125 | 3 | |
| α-helix | 131-138 | 8 | |
| β-strand | 148-150 | 3 | 19 |
| α-helix | 155-159 | 5 | |
| α-helix | 177-182 | 6 | |
| β-strand | 185-187 | 3 | 19 |
Chain D: 7 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 13-16 | 4 | |
| β-strand | 31-39 | 9 | 20 |
| β-strand | 41 | 1 | 21 |
| β-strand | 44 | 1 | 21 |
| α-helix | 49-60 | 12 | |
| β-strand | 66 | 1 | 20 |
| β-strand | 86-91 | 6 | 20 |
| α-helix | 94-102 | 9 | |
| α-helix | 103-107 | 5 | |
| β-strand | 117 | 1 | 22 |
| β-strand | 128-129 | 2 | 20 |
| β-strand | 134 | 1 | 23 |
| α-helix | 143-145 | 3 | |
| β-strand | 151 | 1 | 23 |
| β-strand | 152-158 | 7 | 20 |
| α-helix | 163-174 | 12 | |
| β-strand | 177 | 1 | 22 |
20 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 |
|---|
| Ribosomal 23S RNA | X | RNA | 2880 | Deinococcus radiodurans R1 | |
| 5S ribosomal RNA | Y | RNA | 123 | Deinococcus radiodurans R1 | |
| 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
>3PIP_1 RIBOSOMAL 23S 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
>3PIP_2 5S ribosomal RNA (chains Y)
ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAA
ACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGG
GUU
Sequence of entity 3 (A), FASTA
>3PIP_3 50S ribosomal protein L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK
Sequence of entity 4 (B), FASTA
>3PIP_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASAAKGGK
Sequence of entity 5 (C), FASTA
>3PIP_5 50S ribosomal protein L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ
Sequence of entity 6 (D), FASTA
>3PIP_6 50S ribosomal protein L5 (chains D)
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALI
TLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPN
AFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ
Sequence of entity 7 (E), FASTA
>3PIP_7 50S ribosomal protein L6 (chains E)
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK
HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG
VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATG
GKGKK
Sequence of entity 8 (F), FASTA
>3PIP_8 50S ribosomal protein L11 (chains F)
MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIY
ADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSV
EAAANTVAGTARSMGVTVEGGPNA
Sequence of entity 9 (G), FASTA
>3PIP_9 50S ribosomal protein L13 (chains G)
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIAS
RIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALS
KHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK
Sequence of entity 10 (H), FASTA
>3PIP_10 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL
Sequence of entity 11 (I), FASTA
>3PIP_11 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE
Sequence of entity 12 (J), FASTA
>3PIP_12 50S ribosomal protein L16 (chains J)
MLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRR
GGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRL
AGHKLPIQTKMVKREVYDEAQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 73 |
| LMA | Lankamycin | C43 H74 O15 | 1 |
| LC2 | N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,… | C25 H33 N O7 | 1 |
Water and common crystallization additives (NA, K) are not listed.
Primary citation
Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit. Belousoff, M.J., Shapira, T., Bashan, A. et al. Proc Natl Acad Sci U S A (2011) 108:2717-2722. DOI 10.1073/pnas.1019406108 · 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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