Structure of PDB 4w8f Chain B

Receptor sequence

>4w8fB (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

3D structure

• PDB: 4w8f Allosteric communication in the Dynein motor domain.
• Chain: B
• Resolution: 3.541 Å

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.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ANP	B	L1769 I1770 G1799 G1801 K1802 T1803 N1899 I1929 L1970 R1971 K1974	L405 I406 G435 G437 K438 T439 N535 I565 L606 R607 K610
BS02	ANP	B	F2047 S2048 F2053 G2079 K2080 T2081 A2082 E2195 C2220 K2225 H2228 R2507 R2549 R2552	F677 S678 F683 G709 K710 T711 A712 E825 C850 K855 H858 R1137 R1179 R1182
BS03	ANP	B	I2392 P2420 G2421 S2422 G2423 K2424 T2425 M2426 E2488 I2570 R2620 T2623 R2911	I1022 P1050 G1051 S1052 G1053 K1054 T1055 M1056 E1118 I1200 R1250 T1253 R1541
BS04	ANP	B	M2732 V2733 S2762 R2763 G2765 K2766 T2767 I2768 I2993 R3512	M1362 V1363 S1392 R1393 G1395 K1396 T1397 I1398 I1614 R2037
BS05	MG	B	T2081 E2195 E2511	T711 E825 E1141

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)