Structure of PDB 4w8f Chain A Binding Site BS03

Receptor Information
>4w8f Chain A (length=2608) 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
KDELSKIFDSNSKAIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQA
LILVGKAGCGKTATWKTVIDAMAIFDGHANVVYVIDTKVLTKESLYGSML
KATLEWRDGLFTSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSV
LDDNKILTLPNGERLPIPPNFRILFETDNLDHTTPATITRCGLLWFSTDV
CSISSKIDHLLNKSYEALDNKLSMFELDKLKDLISDSFDMASLTNIFTCS
NDLVHILGVRTFNKLETAVQLAVHLISSYRQWFQNLDDKSLKDVITLLIK
RSLLYALAGDSTGESQRAFIQTINTYFGHDSQELSDYSTIVIANDKLSFS
SFCSEIPSVSLEAHEVMRPDIVIPTIDTIKHEKIFYDLLNSKRGIILCGP
PGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSK
GLTLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTP
ENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLSQ
IYEIYYKAIFKLVPEFRSYTEPFARASVHLYNECKARYSTGLQSHYLFSP
RELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSF
EQLLYETVDKYLPNQDLGNISSTSLLFSGLLSLDFKEVNKTDLVNFIEER
FKTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTIL
TRFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDE
SNILETAFLERMNTLLANADIPDLFQGEEYDKLLNNLRNKTRSLGLLLDT
EQELYDWFVGEIAKNLHVVFTICDPTNNKSSAMISSPALFNRCIINWMGD
WDTKTMSQVANNMVDVIPMEFTDFIVPEVNFTEPIQTIRDAVVNILIHFD
RNFYQKMKVGVNPRSPGYFIDGLRALVKLVTAKYQDLQENQRFVNVGLEK
LNESVLKVNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAK
SELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDA
VRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTP
NRAKRVITTFRTGTWDAYISLVKSLTFEKERWLNTTKQFSKTSQELIGNC
IISSIYETYFGHLNERERADMLVILKRLLGKFAVKYDVNYRFIDYLVTLD
EKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLDPSSHMITVISNYYGN
KTVLLSFLEEGFVKRLENAIRFGSVVIIQDGEFFDPIISRLISREFNHAG
NRVTVEIGDHEVDVSGDFKLFIHSCDPSGDIPIFLRSRVRLVHFVTNKES
IETRIFDITLTEENAEMQRKREDLIKLNTEYKLKLKNLEKRLLEELNNSQ
GNMLENDELMVTLNNLKKEAMNIEKKLSESEEFFPQFDNLVEEYSIIGKH
SVKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFITRVDEILWLLYQEVYC
QFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEAVLTMIGVLSESSDGVP
KLTVDTNDDLRYLWDYVTTKSYISALNWFKNEFFVDEWNIADVVANSENN
YFTMASERDVDGTFKLIELAKASKESLKIIPLGSIENLNYAQEEISKSKI
EGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKFKMFMTCHLTGDKL
PAPLLQRTDRVVYEDIPGILDTVKDLWGSQFFTGKISGVWSVYCTFLLSW
FHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTNNIPWAQ
VRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVRIPQPLL
QQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILDYERLQAKEVASS
TEQLLQEM
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 A 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 G2423 K2424 T2425 M2426 N2536 I2570 R2620 T2623 P2906
Binding residue
(residue number reindexed from 1)		I1023 P1051 G1052 G1054 K1055 T1056 M1057 N1167 I1201 R1251 T1254 P1537
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E3135 D3144
Catalytic site (residue number reindexed from 1) E1668 D1677
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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