Structure of PDB 3vkg Chain A

Receptor sequence

>3vkgA (length=2954) Species: 44689 (Dictyostelium discoideum)

EIDSLKETAWSAIIPAFDHAQNLIKIYLKGNAIITDLHSEAIKDRHWKIL
KKRLNTNWIITELTLGSIWDSDLARNENIYREVITAAQGEIALEEFLKGV
REFWTTLELDLVNYQRKCKLVRGWDDLFNKLAEHLNSISAMKMSPYYKVF
EEEANHWDDRLNKVRSLLDVWIDVQRRWVYLEGIFINQLLPAESTRFKSI
NSEFIAILKKVSGAPLILEVLAIERIQQTMERLSDLLGKVQKALGEYLER
QRSAFARFYFVGDEDLLEIIGNSKDIIKIQKHFRKMFAGLANLTLDDEKT
TIIGMSSAEGETVTFKKPISIANGPKIHEWLTMVESEMKSTLATLLSESL
QHFNQVDVNDHSKYSEWVDNYPTQLVLLTSQIVWSTQVDQALGGGTLQQS
KIQEQLQSIEQTTQMILNNLADSVLQDLSAQKRKKFEHLITELVHQRDVV
RQLQKCKNLTGNKDFDWLYHMRYYYDATQENVLHKLVIHMANATFYYGFE
YLGIGERLVQTPLTDRCYLTLTQALESRMGGNPFGPAGTGKTETVKALGS
QLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLEERILSAV
SQQIQTIQVALKENSKEVELLNISLHQDMGIFVTMNPGYAGRSNLPDNLK
KLFRSMAMIKPDREMIAQVMLYSQGFKTAEVLAGKIVPLFKLCQEQLSAQ
SHYDFGLRALKSVLVSAGGIKRKCQPPDAESKTKADQIYCQYEIGVLLNS
INDTMIPKLVADDIPLIQSLLLDVFPGSQLQPIQMDQLRKKIQEIAKQRH
LVTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDN
IKSEAHVMDPKAITKDQLFGSLDLTTREWTDGLFTATLRRIIDNVRGEST
KRHWIIFDGDVDPEWVENLNSLLDDNKLLTLPNGERLALPNNVRVMFEVQ
DLKYATLATISRCGMVWFSEEILTTQMIFQNYLDTLSNEPFDPQEKEQQK
RNENAIPAGLKVQKECAAIISQYFEPGGLVHKVLEDAGQRPHIMDFTRLR
VLNSFFSLMNRSIVNVIEYNQLHSDFPMSPENQSNYITNRLLYSLMWGLG
GSMGLVERENFSKFIQTIAITPVPANTIPLLDYSVSIDDANWSLWKNKVE
VETHKVASPDVVIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLT
STLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQL
GKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDK
IQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSSLTQIYGTFNRAL
MKLLPNLRSFADNLTDAMVEFYSESQKRFTPDIQAHYIYSPRELSRWDRA
LLEAIQTMDGCTLEGLVRLWAHEALRLFQDRLVETEEKEWTDKKIDEVAL
KHFPSVNLDALKRPILYSNWLTPVNRSDLREYVKARLKVFYPLVLFNEVL
DHILRIDRVFRQPQGHALLIGVSGGGKSVLSRFVAWMNGLSIYTIKYKSS
DFDDDLRMLLKRAGCKEEKICFIFDESNVLESSFLERMNTLLAGGEVPGL
FEGEEFTALMHACKETAQRNGLILDSEEELYKYFTSQVRRNLHVVFTMNP
ASPDFHNSPALFNRCVLDWFGEWSPEALFQVGSEFTRNLDLENPQYIAPP
VFIQEAEILMAIPPSHRDAVVSSLVYIHQTIGEANIRLLKRQGRQNYVTP
RHYLDFINQVVLLINEKRDQLEEEQLHLNIGLKKLRDTEAQVKDLQVSLA
QKNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAV
QKVKAYADLPLREEVEQLENAANELKLKQDEIVATITALEKSIATYKEEY
ATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFNTQMS
TVVGDVVLASAFLAYIGFFDQNFRTDLMRKWMIRLDSVGIKFKSDLSVPS
FLSKPEERLNWHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLM
NQYADKKITKTSFMKNLESALRFGCPLLVQDVESFMIFLFTRDPTAHFTP
DLCSRVTFVNFTVTPSSLQSQCLHEALKTERPDTHKKRSDLLKIQGEFQV
KLRILEKSLLNALSQASGNILDDDSVISTLETLKKETTEIALKVEETETV
MQEISEVSALYNPMALSCSRVYFAMEELSQFHLYQFSLRAFLDIFYNLLN
NNPNLVDKKDPNERLVYLSKDIFSMTFNRVTRTLLNDDKLTFALQLTIIS
VKGTSNEIEESEWDFLLKGGDNLTSIKETIPQLDSLLSTTQQKWLICLRQ
QVPSFSKLVDHIQQNSSDWKQFFGKDQVGEPIIPESWIVAQAQLSNQQST
IVSNFRKILLMKAFHSDRVLQYSHSFVCSVFGEDFLNTLDMANIVEKEVK
SSSPLLLCSVPGYDASSKVDDLALQLHKQYKSFAIGSPEGFELAEKSIYA
AAKSGTWVLLKNIHLAPQWLVQLEKKLHSLSPHPSFRLFMTSEIHPALPA
NLLRMSNVFSYENPPGVKANLLHTFIGIPATRMDKQPAERSRIYFLLAWF
HAIIQERLRYIPLGWTKFFEFNDADLRGALDSIDYWVDLYSKGRSNIDPD
KIPWIAVRTILGSTIYGGRIDNEFDMRLLYSFLEQLFTPSAFNPDFPLVP
SIGLSVPEGTTRAHFMKWIEALPEISTPIWLGLPENAESLLLSNKARKMI
NDLQKMQSSEEDSSSSEDKGKAKPLFRCFEREISTGGKLVKKITNDLANL
LKWYSVPETISLSVWISDFSKRMQQLSEISESVWLGGLLNPEAYITATRQ
SASQLNGRLHASASFNVKGMALEGAVWNNDQLTPTDILSTPISIATLTWK
DPIFNNSSSKLSVPVYLNETRSELLFSIDLPYDQSTSKQNWYQRSVSISS
WKSD

3D structure

• PDB: 3vkg The 2.8 A crystal structure of the dynein motor domain
• Chain: A
• Resolution: 2.81 Å

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	ADP	A	L1947 V1948 G1977 T1978 G1979 K1980 E1982 I2108 L2149 R2150 K2153	L508 V509 G538 T539 G540 K541 E543 I666 L707 R708 K711
BS02	ADP	A	L2249 V2250 W2255 G2279 G2281 K2282 T2283 T2284 E2396 L2421 M2425 N2429 R2809	L801 V802 W807 G831 G833 K834 T835 T836 E948 L973 M977 N981 R1324
BS03	ADP	A	V2647 I2648 G2677 S2678 G2679 K2680 T2681 M2682 I2827 P2876 R2877 S2880	V1162 I1163 G1192 S1193 G1194 K1195 T1196 M1197 I1342 P1391 R1392 S1395
BS04	ADP	A	L2988 V2989 G3019 G3020 G3021 K3022 S3023 V3024 W3176	L1493 V1494 G1524 G1525 G1526 K1527 S1528 V1529 W1673
BS05	MG	A	T2283 E2396	T835 E948

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0008569 minus-end-directed microtubule motor activity
• 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

Cellular Component

• GO:0030286 dynein complex

External links

• PDB: RCSB:3vkg, PDBe:3vkg, PDBj:3vkg
• PDBsum: 3vkg
• PubMed: 22398446
• UniProt: P34036|DYHC_DICDI Dynein heavy chain, cytoplasmic (Gene Name=dhcA)