Structure of PDB 5mmi Chain D Binding Site BS01

Receptor Information

>5mmi Chain D (length=221) Species: 3562 (Spinacia oleracea)

SVDAGIGVMGTKLGMMSFFEEDGTVVPVTVIGFKEGNIVTQVKTESTDGY
NAVQVGYERLRDRKLTMPERGHLNKAGVIPMRHLQEFRLVSVDDFTPSQK
LLFEELFKEGDMVDISGTTIGKGFQGGIKRHNFKRGLMTHGSKSHRALGS
IGAGTTPGHVYKGKKMPGRMGGTKTKIRKLKIMKIDTDLRVVMIKGAVPG
KPGNLLRLAPAKIVGKNIPKN

Ligand information

>5mmi Chain A (length=2798)

ucaaacgaggaaaggcuuacgguggauaccuaggcacccagagacgagga
agggcguauuaaucgacgaaaugcuucggggaguugaaaauaagcagaga
uccggagauucccgaauaggucaaccuuucgaacuucugcugaauccaug
ggcaggcaagagacaaccuggcgaacugaaacaucuuaguagccagagga
aaagaaagcaaaagcgauucccguaguagcggcgagcgaaaugggagcag
ccuaaaccgugaaaacgggguugugggagagcaauacaagcgucgugcug
cuaggcgaaucaguggagugcggaacccuagauggugaaaguccaguagc
cgaaagcaucacuagcuuaugcucugacccgaguagcauggggcacgugg
aaucccgugugaaucagcaaggaccaccuugcaaggcuaaauacuccugg
gugaccgauagcgaaguaguaccgugagggaagggugaaaagaaccccca
ucggggagugaaaagaacaugaaaccguaagcucucaagcagugggaggg
ggaccagacccugaccgcgugccuguugaagaaugagccggcgacucaua
ggcaguggcuugguuaagggaacccaccggagccguagcgaaagcgaguc
uucauagggcaauugucacugcuuauggacccgaaccugggugaucuauc
caugaccaggaugaagcuugggugaaacuaaguggagguccgaaccgacu
gauguugaagaaucagcggaugaguugugguuaggggugaaaugccacuc
gaacccagagcuagcugguucuccccgaaaugcguugaggcgcagcaguu
gacuggacaucuagggguaaagcacuguuucggugcgggccgccgguacc
aaaucgaggcaaacucugaauacuagauaugaccuccaaauaacaggggu
caaggucggccagugagacgaugggggauaagcuucaucgucgagaggga
aacagcccggaucaccagcuaaggccccuaaaugaccgcucagugauaaa
ggagguaggggugcagagacagccaggagguuugccuagaagcagccacc
cuugaaagagugcguaauagcucacugaucgagcgcucuugcgccgaaga
ugaacggggcuaagcggucugccgaagcugugggauguaaaaaaacaucg
guaggggagcguuccguguuagggagaaacgcgugcgugagccgcguugg
acgaagcggaagcgagaaugucggcuugaguaacgcaaacauuggugaga
auccaaugccccgaaaaccuaaggguuccuccgcaagguucguccacgga
gggugagucagggccuaagaucaggccgaaaggcguagucgauggacaac
aggugaauauuccuguacuaccccuuguuggucccgagggacggaggagg
cuagguuagccgaaagaugguuaucgguucaaggacgcaaggugacccug
uuuuucaggguaagaagggguagagaaaaugccucgagccaauguucgag
uaccaggcgcuacggcgcugaaguaaccgaugccauacucccaggaaaag
cucgaacgaccuucaacaaaaggguaccuguacccgaaaccgacacaggu
agguagguagagaauaccuaggggcgcgagacaacucucucuaaggaacu
cggcaaaauagccccguaacuucgggagaaggggugcccccucggggguc
gaagugaccaggcccgggcgacuguuuaccaaaaacacaggucuccgcaa
agucguaagaccauguaugggggcugacgccugcccagugccggaagguc
aaggaaguuggugaccugaugacaggggagccggcgaccgaagccccggu
gaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgacccgcacgaaaggcguaacgaucugggcacugucucgg
agagaggcucggugaaauagacaugucugugaagaugcggacuaccugca
ccuggacagaaagacccuaugaagcuuuacuguucccugggauuggcuuu
gggcuuuuccugcgcagcuuagguggaaggcgaagaaggcccccuuccgg
gggggcccgagccaucagugagauaccacucuggaagagcuagaauucua
accuugugucaggaccuacgggccaagggacauucucagguagacaguuu
cuauggggcguaggccucccaaaagguaacggaggcgugcaaagguuucc
ucgggccggacggagauuggcccucgagugcaaaggcagaagggagcuug
acugcaagacccacccgucgagcagggacgaaagucggccuuagugaucc
gacggugccgaguggaagggccgucgcucaacggauaaaaguuacucuag
ggauaacaggcugaucuuccccaagaguucacaucgacgggaagguuugg
caccucgaugucggcucuucgccaccuggggcuguaguauguuccaaggg
uugggcuguucgcccauuaaagcgguacgugagcuggguucagaacgucg
ugagacaguucgguccauauccggugugggcguuagagcauugagaggac
cuuucccuaguacgagaggaccgggaaggacgcaccucugguguaccagu
uaucgugcccacgguaaacgcuggguagccaagugcggagcggauaacug
cugaaagcaucuaaguaguaagcccaccccaagaugagugcucuccua

.............<<<<<<<<<<.....<<..<<<<<<<<<<<.<.....
.<<<<<<..[..((.>>>.....<<<<<<<..<<.))..]...>>.....
>>>>>>>...>>>....<<<....>>>......<<<<<<<<.........
>>>>>..>>>.>....<<<<<<.....<<....>>......>>>>>.>..
.......<<....>>..<<<<<<.....<<.....>>....>>>>>>..<
<<....<<<<....>>>>......<<<<<<<<<....<<<<.....<.<<
<<.<<<...<<.<<.....>>.>>((......<<<.....))>>>...>>
>...>>>>.>....>>>>.>>>>>>..>>>.....<<<<<<<<.......
..>>>>>>>>......<<<<<..<<<<>>>>>..>>>......>>.>>>>
>>>.>>...............<<....>>....>>.........<<<<..
..>>>>.................>>>>>>>>>>........<<<<..<<<
<.......>>>>..>>>>...<.<........>.>.<<<<<<....<<<<
<<<<<<<<...<<<...<<.......>>...>>>...<<....>>..<<<
<.....>>>>.....>>>>>>>>>>>>..<<.<...<<<<<<.....<.<
<<<<<<..<<<....<<<<<<......>>>>>>.....>>>...<<<.<<
<<<........>>>>>>>>....>>>>>>>.>...<<<.....>>>....
..>>>>>>......>.>>..<<<<<<....<<<<<....>>>>><<.<<<
<<<<....<<<<<<......<<...<<<<<<<<<..<<<<<...>>>.>>
..>>>>>>>>>..>>.......>>>>>>..<<<<<<.........>>>>>
>..>>>>>>>..>>..<<<<<<<<<<......>>>>>>>>>>....<<<.
.....>>>...<<<<.<<<...<<<(((.....<<<<<<...........
<<..<<<<<<<<<<.......<.<<<.<<<...<<.........>>...>
>>.........<<......>>...>>>.>...>>>>>>>>>>.>>.....
.....))).....>>>>>>.>>>...>>>>>>><<<<<......>>>>>.
...>>>>>><.<<<<<<...........<<<<<.<<....>>>>>>.>..
.....>>>>>>..>.....>>>>>><......<<.....<<<<<<.....
..>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>
>>....((<<<<.<<...<<<...<<<....>>>...>>>...>>...<<
<<<........>>>>>))<<<<<.<<<<.<<<<.<<<<....<<<<..<<
<..<<<<<<<<<<.....(((..>>>>>....<<<<<...<<<.<<<<<<
.....>>>>>>.....<<<<<<.......>>>>>>..>>>..>>>>>...
..<..<<<<<....>>>>>...>>>>>>...>>>...>>>>.........
>>>>...>>>>....>>>>..>>>>>>>>>..>>.....<<......>>>
>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<.....
....<.....<<<<<...............>>>>><<<<<<..>>>>>>.
...........<<<<<<<<<..<<<.........>>>..<<<<<<<....
.<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<.
..<<..<<<<<<..<<<<....>>>>...>>>>>>..>>...>>>>>>>>
..>>>>><<<<<<.......>>>>>>........<...........<<<<
<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>
>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<
<<.<<<..<......<<<<.<<<<<<..<<<<<..<<<<<<<..<<.<<<
.<<<<<<<<<............<<<<..<<<......<<<<<<<<....>
>>>>>>>...>>>............>>>.>..>>>>>>>>>.>>>.>>..
.<<<<<.<<<..........>>>>>>>>.....>>>>>>>...>>>>>..
<<<<.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<
..<<<<<<<.......>>>>>>>....<<...(((>>....>>>>>>>..
.<<<<..<<<......>>>..>>>>.<<<....>>>.>>))).......<
<<<<<<.<<..>>>>..>>>>>>>>>.............>>>>..>>>>>
>.......<<<<...<<<<<<...<<.......>>...>>>>>>....>>
>.>.......<<<<<.<.<<<<..<<<<<<<<........>>>>>..>>>
.<<<<<.....>>>>>.....>>>>...>...>>>>>.....<<<<<<<.
...>>>.>>>>....>...>>>>>>>>>>>....<<<<<<<...<.<<..
<<<<<<<...............>>>>>>>.<<<<<...<<<<...<<<<<
<<<<<<))).>>>>>>...>>>>>...>>>>.>>>>>..<.<<...<<<<
<<...........>>>>>>...>>>.>>.>.......>>>>>>>....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mmi The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): M99 S101 P111 Y134 Q138 P152 E153 G155 H156 K159 E170 R172 T203 I204 F208 G210 K213 R214 N216 F217 K218 R219 M222 T223 H224 G225 S226 K227 H229 R230 G233 S234 I235 A237 G238 T239 T240 P241 G242 H243 V244 K246 G247 K248 M250 P251 R253 K258 T259 K260 K263 K279 A281 V282 P283 G284 K285 K296 V298 K304 N305
• Binding residue (residue number reindexed from 1): M15 S17 P27 Y50 Q54 P68 E69 G71 H72 K75 E86 R88 T119 I120 F124 G126 K129 R130 N132 F133 K134 R135 M138 T139 H140 G141 S142 K143 H145 R146 G149 S150 I151 A153 G154 T155 T156 P157 G158 H159 V160 K162 G163 K164 M166 P167 R169 K174 T175 K176 K179 K195 A197 V198 P199 G200 K201 K212 V214 K220 N221

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0009507 chloroplast
• GO:0009941 chloroplast envelope
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mmi, PDBe:5mmi, PDBj:5mmi
• PDBsum: 5mmi
• PubMed: 28007896
• UniProt: P82191|RK3_SPIOL Large ribosomal subunit protein uL3c (Gene Name=RPL3)