Structure of PDB 7yp3 Chain D Binding Site BS02

Receptor Information
>7yp3 Chain D (length=408) Species: 911111 (Streptomyces sp. SCSIO 01934) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMRILFATVSEKSHLFTMVPLAWSLAAAGHEVHVASNPALTASIKSTGL
TAVPVGKDHNLHEMLTENRDSLENPLSDWSTPELDRHSWEQVLMKFKVSV
MFAYQTYNDCMVHELVDYARHWQPDLVIWDPVTYAGPVAARVVGAAHARL
LWCIDIYAKMREVFLARLAEQPEERREDPMADWLGGILGRYGHTFDEEVV
VGQWTIDQIPTSLQLPLSLRRVPVRYLPHNGPSEIPDWLREAPGRPRVVL
TSFMPVADMINTLGSMDIDVVAALPPEEVEALEKVPANTRIVDFVPLHAL
LPGASVLIHHGGFGSWGTALVNGVPQFIPTIRYADWWNKGTSLHEAGAGL
VVHASELTAEVLRESVERLVEDASYREAAERLREENQRTPTPHDVVPVIE
ELTAEHGR
Ligand information
Ligand IDELO
InChIInChI=1S/C54H88O18/c1-13-37-33(9)71-53(63,25-41(37)67-45-23-39(55)49(61)35(11)65-45)31(7)47(59)29(5)51-27(3)19-15-17-22-44(58)70-52(28(4)20-16-18-21-43(57)69-51)30(6)48(60)32(8)54(64)26-42(38(14-2)34(10)72-54)68-46-24-40(56)50(62)36(12)66-46/h15-22,27-42,45-52,55-56,59-64H,13-14,23-26H2,1-12H3/b19-15+,20-16+,21-18+,22-17+/t27-,28-,29-,30-,31-,32-,33+,34+,35-,36-,37+,38+,39-,40-,41+,42+,45-,46-,47+,48+,49+,50+,51-,52-,53+,54+/m0/s1
InChIKeyOSERMIPXNLXAPD-MJMYBOKFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCC1C(OC(CC1OC2CC(C(C(O2)C)O)O)(C(C)C(C(C)C3C(C=CC=CC(=O)OC(C(C=CC=CC(=O)O3)C)C(C)C(C(C)C4(CC(C(C(O4)C)CC)OC5CC(C(C(O5)C)O)O)O)O)C)O)O)C
OpenEye OEToolkits 2.0.7CC[C@H]1[C@@H](C[C@](O[C@@H]1C)(O)[C@H]([C@H](O)[C@@H]([C@H]2OC(=O)/C=C/C=C/[C@@H]([C@H](OC(=O)/C=C/C=C/[C@@H]2C)[C@H]([C@@H](O)[C@@H]([C@@]3(O[C@@H]([C@H]([C@@H](C3)O[C@@H]4O[C@H]([C@H]([C@H](C4)O)O)C)CC)C)O)C)C)C)C)C)O[C@@H]5O[C@H]([C@H]([C@H](C5)O)O)C
CACTVS 3.385CC[CH]1[CH](C)O[C](O)(C[CH]1O[CH]2C[CH](O)[CH](O)[CH](C)O2)[CH](C)[CH](O)[CH](C)[CH]3OC(=O)C=CC=C[CH](C)[CH](OC(=O)C=CC=C[CH]3C)[CH](C)[CH](O)[CH](C)[C]4(O)C[CH](O[CH]5C[CH](O)[CH](O)[CH](C)O5)[CH](CC)[CH](C)O4
CACTVS 3.385CC[C@@H]1[C@@H](C)O[C@](O)(C[C@H]1O[C@H]2C[C@H](O)[C@H](O)[C@H](C)O2)[C@@H](C)[C@H](O)[C@H](C)[C@H]3OC(=O)/C=C/C=C/[C@H](C)[C@H](OC(=O)\C=C\C=C\[C@@H]3C)[C@@H](C)[C@@H](O)[C@H](C)[C@@]4(O)C[C@@H](O[C@H]5C[C@H](O)[C@H](O)[C@H](C)O5)[C@H](CC)[C@@H](C)O4
FormulaC54 H88 O18
NameElaiophylin;
(3~{E},5~{E},7~{S},8~{S},11~{E},13~{E},15~{S},16~{S})-8,16-bis[(2~{S},3~{R},4~{S})-4-[(2~{R},4~{R},5~{R},6~{R})-5-ethyl-6-methyl-4-[(2~{R},4~{S},5~{S},6~{S})-6-methyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-oxan-2-yl]-3-oxidanyl-pentan-2-yl]-7,15-dimethyl-1,9-dioxacyclohexadeca-3,5,11,13-tetraene-2,10-dione
ChEMBLCHEMBL3740707
DrugBank
ZINC
PDB chain7yp3 Chain E Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7yp3 Substrate-induced dimerization of elaiophylin glycosyltransferase reveals a novel self-activating form of glycosyltransferase for symmetric glycosylation.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
L70 N72 L74 S75 V96 M99 F100
Binding residue
(residue number reindexed from 1)
L72 N74 L76 S77 V98 M101 F102
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008194 UDP-glycosyltransferase activity
GO:0016740 transferase activity
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
Biological Process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:7yp3, PDBe:7yp3, PDBj:7yp3
PDBsum7yp3
PubMed36189743
UniProtE5L4T5

[Back to BioLiP]