Structure of PDB 8wgo Chain A Binding Site BS02

Receptor Information

>8wgo Chain A (length=869) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MDYNFNLEHPFFFTNNDYSTDTSIKYQASLPFNWHEVMNNDEWVYQYPIG
KFVERQGWKIHISSEYNSSHELLQDVAKICHEMRIPFKHLSTEDKFIMRN
GKLVSRGFSGKFITCYPNQNELESVLQRLESALKQYNGPYILSDKRWDEA
PIYLRYGVFRPSRDDEKKVAIDELIVGDEVVKDERLPVFKIPKGIVPPDF
LNKWLDKKDKKQGDFPFIIDNAIRFSNSGGIYNARLKEDGKKIILKEARP
YTGLGFDGTYSSEKLASECKALKILNEWSEAPKIYWHGKIWEHTFLGIEH
MKGVPLNRWVTNNFPLYEVVDKTKDYLLRVSKIVEKLIDLTNKFHSENVY
HQDLHLGNILVKDEDEISIIDWEQAVFSNDEKVVHKVAAPGFRAWRETLP
SEIDWYGIRQIAHYLYMPLVTTSDLTYNYVSQTRIEGKKLFESLGYTREH
IDYVESLLSYLDSKCPQIENISRKKVLKPMHEIRTIESEQDIQDFIIKLL
RGFTLTYGQWRKEFQSRFFPVHYYGLNFNQGIAFSDLAILWSYQQLAKKV
KNFKFDDYYEIRTQVINEAVNNFKKSSLSGLFDGKIGTIWLIYEFGEIDR
AVELFTTHFIEIFENSQNKNLYSGQAGILLVGLYFLSKGEIDNKLGEEIL
IRLREYTLNYIENPETFCKVGASDVQSNDPYENFGGLLYGHAGVAWLFGE
AYKLTGESIYKNGLELAVDKELVAYKVDSNNSLQYSQGHRLLPYLATGSA
GLLLLINRNKEILSSKYLKYLTSLERATDVVFCVLPGLFNGFCGLEVANN
IYSDIDDNFSGQKKLIEQLYRYLCVIEEGFVIAGDNGLKITTDIASGFAG
VAIGLVSIMDNKLTILPQI

Ligand information

Ligand ID

GSP

InChI

InChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

InChIKey

XOFLBQFBSOEHOG-UUOKFMHZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04	S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O

Formula

C10 H16 N5 O13 P3 S

Name

5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

PDB chain

8wgo Chain A Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8wgo Mechanistic insights into lanthipeptide modification by a distinct subclass of LanKC enzyme that forms dimers.
Resolution	3.7 Å
Binding residue (original residue number in PDB)	R224 H300 M301
Binding residue (residue number reindexed from 1)	R224 H300 M301
Annotation score	1

External links

PDB	RCSB:8wgo, PDBe:8wgo, PDBj:8wgo
PDBsum	8wgo
PubMed	39154050
UniProt	A0A2U3S0J5

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