Structure of PDB 5yij Chain A Binding Site BS01

Receptor Information
>5yij Chain A (length=959) Species: 446 (Legionella pneumophila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFSLYTDDTVKAAAQYAYDNYLGKPYTGSVESAPANFGGRMVYRQHHGLS
HTLRTMAYAELIVEEARKAKLRGETLGKFKDGRTIADVTPQELKKIMIAQ
AFFVAGRDDEASDAKNYQKYHEQSRDAFLKYVKDNESTLIPDVFKDQEDV
NFYARVIEDKSHDWESTPAHVLINQGHMVDLVRVKQPPESFLQRYFSSMQ
RWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKEPHLVVSGLGRYVIGE
DGQPIREAPKKGQKEGDLKVFPQTYKNERLMRVDEFLKLPEIQNTFPGSG
KHLQGGMPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPI
KQAFQSSKGKERRQPNVDEIAAARIIQQILANPDCIHDDHVLINGQKLEQ
QFFRDLLAKCEMAVVGSLLNDTDIGNIDTLMRHEKDTEFHSTNPEAVPVK
IGEYWINDQRINNSSGNITQKKHDLIFLMQNDAWYFSRVNAIAQNRDKGS
TFKEVLITTLMTPLTSKALVDTSQAKPPTRLFRGLNLSEEFTKGLIDQAN
AMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEIKLVKETWD
SNVIFEMLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVALVPVKVTLDGK
TQKGENRYVFTFVAVKSPDFTPRHESGYAVEPFLRMQAAKLAEVKSSIEK
AQRAPDLETIFNLQNEVEAVQYSHLSTGYKNFLKNTVGPVLENSLSGLME
SDTDTLSKALAAFPSDTQWSAFNFEEARQAKRQMDAIKQMVGNKVVLDAL
TQCQDALEKQNIAGALDALKKIPSEKEMGTIRRELREQIQSARQELESLQ
RAVVTPVVTDEKKVRERYDALIENTSKKITELETGKLPNLDAVKKGISNL
SNLKQEVTVLRNEKIRMHVGTDKVDFSDVEKLEQQIQVIDTKLADAYLLE
VTKQISALE
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain5yij Chain A Residue 1201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5yij Structural basis of ubiquitin modification by the Legionella effector SdeA.
Resolution3.18 Å
Binding residue
(original residue number in PDB)		Q713 F719 N723 Q727 R729 R766 G767 N769 S820 T822 W832 E862
Binding residue
(residue number reindexed from 1)		Q480 F486 N490 Q494 R496 R533 G534 N536 S587 T589 W599 E629
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=3.42,Kd=381uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0106274 NAD+-protein-arginine ADP-ribosyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:5yij, PDBe:5yij, PDBj:5yij
PDBsum5yij
PubMed29795342
UniProtQ6RCR0

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