Structure of PDB 4w8f Chain B Binding Site BS05

Receptor Information

>4w8f Chain B (length=2609) Species: 10665,559292

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 ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 4w8f Chain B Residue 5005

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4w8f Allosteric communication in the Dynein motor domain.
• Resolution: 3.541 Å
• Binding residue (original residue number in PDB): T2081 E2195 E2511
• Binding residue (residue number reindexed from 1): T711 E825 E1141
• Annotation score: 1

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

External links

• PDB: RCSB:4w8f, PDBe:4w8f, PDBj:4w8f
• PDBsum: 4w8f
• PubMed: 25417161
• UniProt: P00720|ENLYS_BPT4 Endolysin (Gene Name=E);
  P36022|DYHC_YEAST Dynein heavy chain, cytoplasmic (Gene Name=DYN1)