Structure of PDB 4w8f Chain B Binding Site BS03

Receptor Information
>4w8f Chain B (length=2609) Species: 10665,559292 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVIEKSLNRIKKFWKEAQYEVIEHSSGLKLVREWDVLEQACKEDLEELVS
MKASNYYKIFEQDCLDLESKLTKLSEIQVNWVEVQFYWLDLYGILGENLD
IQNFLPLETSKFKSLTSEYKMITTRAFQLDTTIEVIHIPNFDTTLKLTID
SLKMIKSSLSTFLERQRRQFPRFYFLGNDDLLKIIGSGKHHDQVSKFMKK
MFGSIESIIFLEDFITGVRSVEGEVLNLNEKIELKDSIQAQEWLNILDTE
IKLSVFTQFRDCLGQLKDGTDIEVVVSKYIFQAILLSAQVMWTELVEKCL
QTNQFSKYWKEVDMKIKGLLDKLNKSSDNVKKKIEALLVEYLHFNNVIGQ
LKNCSTKEEARLLWAKVQKFYQKNDTLDDLNSVFISQSGYLLQYKFEYIG
IPERLIYTPLLLIGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLG
RVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDQFNRLDEKVLSAVSAN
IQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKK
SFREFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCSSMN
HYHFGLRTLKGVLRNCSPLISEFGEGEKTVVESLKRVILPSLGDTDELVF
KDELSKIFDNSKAIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQAL
ILVGKAGCGKTATWKTVIDAMAIFDGHANVVYVIDTKVLTKESLYGSMLK
ATLEWRDGLFTSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVL
DDNKILTLPNGERLPIPPNFRILFETDNLDHTTPATITRCGLLWFSTDVC
SISSKIDHLLNKSYEALDNKLSMFELDKLKDLISDSFDMASLTNIFTCSN
DLVHILGVRTFNKLETAVQLAVHLISSYRQWFQNLDDKSLKDVITLLIKR
SLLYALAGDSTGESQRAFIQTINTYFGHDSQELSDYSTIVIANDKLSFSS
FCSEIPSVSLEAHEVMRPDIVIPTIDTIKHEKIFYDLLNSKRGIILCGPP
GSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKG
LTLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPE
NKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLSQI
YEIYYKAIFKLVPEFRSYTEPFARASVHLYNECKARYSTGLQSHYLFSPR
ELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSFE
QLLYETVDKYLPNQDLGNISSTSLLFSGLLSLDFKEVNKTDLVNFIEERF
KTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTILT
RFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDES
NILETAFLERMNTLLANADIPDLFQGEEYDKLLNNLRNKTRSLGLLLDTE
QELYDWFVGEIAKNLHVVFTICDPTNNKSSAMISSPALFNRCIINWMGDW
DTKTMSQVANNMVDVIPMEFTDFIFTEPIQTIRDAVVNILIHFDRNFYQK
MKVGVNPRSPGYFIDGLRALVKLVTAKYQDLQENQRFVNVGLEKLNESVL
KVNENIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELD
KAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRA
ALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAK
RVITTFRTGTWDAYGSGSGSSISLVKSLTFEKERWLNTTKQFSKTSQELI
GNCIISSIYETYFGHLNERERADMLVILKRLLGKFAVKYDVNYRFIDYLV
TLDEKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLDPSSHMITVISNY
YGNKTVLLSFLEEGFVKRLENAIRFGSVVIIQDGEFFDPIISRLISREFN
HAGNRVTVEEVDVSGDFKLFIHSCDPSGDIPIFLRSRVRLVHFVTNKESI
ETRIFDITLTEENAEMQRKREDLIKLNTEYKLKLKNLEKRLLEELNNSQG
NMLENDELMVTLNNLKKEAMNIEKKLSESEEFFPQFDNLVEEYSIIGKHS
VKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFIKKTRVDEILWLLYQEVY
CQFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEAVLTMIGVLSESSDGV
PKLTVDTNDDLRYLWDYVTTKSYISALNWFKNEFFVDEWNIADVVANSEN
NYFTMASERDVDGTFKLIELAKASKESLKIIPLGSIENLNYAQEEISKSK
IEGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKFKMFMTCHLTGDK
LPAPLLQRTDRVVYEDIPGILDTVKDLWGSQFFTGKISGVWSVYCTFLLS
WFHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTNNIPWA
QVRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVRIPQPL
LQQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILDYERLQAKEVAS
STEQLLQEM
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain4w8f Chain B Residue 5003 [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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PDB4w8f Allosteric communication in the Dynein motor domain.
Resolution3.541 Å
Binding residue
(original residue number in PDB)		I2392 P2420 G2421 S2422 G2423 K2424 T2425 M2426 E2488 I2570 R2620 T2623 R2911
Binding residue
(residue number reindexed from 1)		I1022 P1050 G1051 S1052 G1053 K1054 T1055 M1056 E1118 I1200 R1250 T1253 R1541
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E3135 D3144
Catalytic site (residue number reindexed from 1) E1664 D1673
Enzyme Commision number 3.2.1.17: lysozyme.
Gene Ontology
Molecular Function
GO:0003796 lysozyme activity
GO:0005524 ATP binding
GO:0008569 minus-end-directed microtubule motor activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016887 ATP hydrolysis activity
GO:0045505 dynein intermediate chain binding
GO:0051959 dynein light intermediate chain binding
Biological Process
GO:0007018 microtubule-based movement
GO:0009253 peptidoglycan catabolic process
GO:0016998 cell wall macromolecule catabolic process
GO:0031640 killing of cells of another organism
GO:0042742 defense response to bacterium
GO:0044659 viral release from host cell by cytolysis
Cellular Component
GO:0030286 dynein complex
GO:0030430 host cell cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4w8f, PDBe:4w8f, PDBj:4w8f
PDBsum4w8f
PubMed25417161
UniProtP00720|ENLYS_BPT4 Endolysin (Gene Name=E);
P36022|DYHC_YEAST Dynein heavy chain, cytoplasmic (Gene Name=DYN1)

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