Structure of PDB 5lzs Chain jj Binding Site BS06

Receptor Information

>5lzs Chain jj (length=441) Species: 9986 (Oryctolagus cuniculus)

EKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGS
FKYAWVLDKLKAERERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMI
TGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVN
KMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLE
PSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDV
YKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEAL
PGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQI
SAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVD
MVPGKPMCVESFSDYPPLGRFAVRDMRQTVAVGVIKAVDKK

Ligand information

• Ligand ID: 7C4
• InChI: InChI=1S/C57H89N7O15/c1-15-33(8)46-44(66)29-45(67)79-49(32(6)7)48(68)34(9)50(69)58-39(26-30(2)3)54(73)64-25-17-19-41(64)56(75)62(13)43(28-37-20-22-38(77-14)23-21-37)57(76)78-36(11)47(52(71)59-46)60-51(70)42(27-31(4)5)61(12)55(74)40-18-16-24-63(40)53(72)35(10)65/h20-23,30-36,39-44,46-47,49,65-66H,15-19,24-29H2,1-14H3,(H,58,69)(H,59,71)(H,60,70)/t33-,34-,35-,36+,39-,40-,41-,42+,43-,44-,46+,47-,49-/m0/s1
• InChIKey: KYHUYMLIVQFXRI-SJPGYWQQSA-N
• SMILES:
  : CC[C@H](C)[C@@H]1[C@H](CC(=O)O[C@H](C(=O)[C@@H](C(=O)N[C@H](C(=O)N2CCC[C@H]2C(=O)N([C@H](C(=O)O[C@@H]([C@@H](C(=O)N1)NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@@H]3CCCN3C(=O)[C@H](C)O)C)Cc4ccc(cc4)OC)C)CC(C)C)C)C(C)C)O
  CACTVS 3.385: CC[CH](C)[CH]1NC(=O)[CH](NC(=O)[CH](CC(C)C)N(C)C(=O)[CH]2CCCN2C(=O)[CH](C)O)[CH](C)OC(=O)[CH](Cc3ccc(OC)cc3)N(C)C(=O)[CH]4CCCN4C(=O)[CH](CC(C)C)NC(=O)[CH](C)C(=O)[CH](OC(=O)C[CH]1O)C(C)C
  : CC[C@H](C)[C@H]1NC(=O)[C@@H](NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@@H]2CCCN2C(=O)[C@H](C)O)[C@@H](C)OC(=O)[C@H](Cc3ccc(OC)cc3)N(C)C(=O)[C@@H]4CCCN4C(=O)[C@H](CC(C)C)NC(=O)[C@@H](C)C(=O)[C@@H](OC(=O)C[C@@H]1O)C(C)C
  OpenEye OEToolkits 2.0.6: CCC(C)C1C(CC(=O)OC(C(=O)C(C(=O)NC(C(=O)N2CCCC2C(=O)N(C(C(=O)OC(C(C(=O)N1)NC(=O)C(CC(C)C)N(C)C(=O)C3CCCN3C(=O)C(C)O)C)Cc4ccc(cc4)OC)C)CC(C)C)C)C(C)C)O
• Formula: C57 H89 N7 O15
• Name: (2~{S})-~{N}-[(2~{R})-1-[[(3~{S},6~{S},8~{S},12~{S},13~{R},16~{S},17~{R},20~{S},23~{S})-13-[(2~{S})-butan-2-yl]-20-[(4-methoxyphenyl)methyl]-6,17,21-trimethyl-3-(2-methylpropyl)-12-oxidanyl-2,5,7,10,15,19,22-heptakis(oxidanylidene)-8-propan-2-yl-9,18-dioxa-1,4,14,21-tetrazabicyclo[21.3.0]hexacosan-16-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-~{N}-methyl-1-[(2~{S})-2-oxidanylpropanoyl]pyrrolidine-2-carboxamide
• ChEMBL: CHEMBL414042
• PDB chain: 5lzs Chain jj Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5lzs Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes.
• Resolution: 3.31 Å
• Binding residue (original residue number in PDB): L138 Y141 I181 Q343 I345 R381 R382 S383 R423 V435 G436
• Binding residue (residue number reindexed from 1): L135 Y138 I178 Q340 I342 R378 R379 S380 R420 V432 G433
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.6.5.-

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0019001 guanyl nucleotide binding
• GO:0019900 kinase binding
• GO:0019901 protein kinase binding
• GO:0060090 molecular adaptor activity

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0044829 positive regulation by host of viral genome replication
• GO:0071364 cellular response to epidermal growth factor stimulus

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005886 plasma membrane
• GO:0022626 cytosolic ribosome
• GO:0030864 cortical actin cytoskeleton
• GO:0032587 ruffle membrane

External links

• PDB: RCSB:5lzs, PDBe:5lzs, PDBj:5lzs
• PDBsum: 5lzs
• PubMed: 27863242
• UniProt: P68105|EF1A1_RABIT Elongation factor 1-alpha 1 (Gene Name=EEF1A1)