3VKH: Functional full-length dynein motor domain

X-ray structure of a functional full-length dynein motor domain. Determined by X-ray diffraction at 3.8 Å resolution. Released 14 Mar 2012.

Method
X-ray diffraction
Resolution
3.8 Å
Organism
Dictyostelium discoideum
Chains
2
Atoms
45,974
Mol. weight
772.08 kDa
Ligands
ADP
Released
14 Mar 2012

Explore 3VKH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VKH contains 296 α-helices and 158 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 157 helices, 81 β-strands

ElementResiduesLengthSheet
α-helix1513-153725
β-strand154211
β-strand1545-154842
β-strand1552-155542
α-helix1558-157417
α-helix1575-15773
α-helix1585-161632
α-helix1626-16283
α-helix1630-165223
β-strand165511
α-helix1656-16594
α-helix1665-169329
α-helix1695-16995
α-helix1702-17109
α-helix1716-17194
α-helix1722-17243
β-strand1729-173463
β-strand1740-174673
β-strand1751-175993
α-helix1766-179227
α-helix1800-18078
α-helix1812-182918
β-strand183314
α-helix1838-186225
α-helix1869-189224
β-strand190014
α-helix1904-19074
β-strand1910-191345
β-strand1926-192945
β-strand1932-193545
α-helix1951-196414
β-strand1969-197356
α-helix1980-199011
β-strand1995-199956
α-helix2006-201510
α-helix2016-20205
β-strand2022-202656
α-helix2028-20303
α-helix2033-205018
β-strand2056-205727
β-strand2065-206627
β-strand2072-207546
β-strand207716
β-strand208118
β-strand208418
β-strand2095-209956
α-helix2105-211410
α-helix2121-213515
α-helix2149-216315
α-helix2178-220225
α-helix2211-222212
α-helix2234-224613
α-helix2253-226614
β-strand2271-227339
α-helix2282-229615
β-strand2301-230339
α-helix2313-23164
β-strand2319-2321310
β-strand2326-2328310
α-helix2331-234010
α-helix2346-23483
β-strand2350-235569
α-helix2365-23673
α-helix2368-23714
β-strand2376111
β-strand2386111
β-strand2391-239559
β-strand2412-241329
α-helix2418-24203
α-helix2423-243412
α-helix2441-24488
α-helix2490-250617
α-helix2511-252111
β-strand2524112
α-helix2530-255122
α-helix2562-258019
β-strand2585112
α-helix2587-260014
α-helix2612-26143
β-strand2615113
β-strand2626113
β-strand2637114
β-strand2640114
α-helix2651-266515
β-strand2671-2673315
α-helix2680-26878
α-helix2688-26903
β-strand2694-2699615
α-helix2707-27148
β-strand2718-2721416
β-strand2729-2732416
β-strand2738-2743615
α-helix2758-27647
α-helix2765-27695
β-strand2771-2774416
β-strand2779-2783516
β-strand2786-2792715
α-helix2805-28084
β-strand2813115
α-helix2821-283515
α-helix2840-28423
α-helix2846-286318
α-helix2876-289015
α-helix2898-291316
α-helix2920-293718
α-helix2943-29464
α-helix29471
β-strand2952-2953217
β-strand2961-2962217
α-helix2965-298218
α-helix2992-300514
β-strand3012-3015418
β-strand3016119
α-helix3022-303211
β-strand3036-3038318
α-helix3048-306316
β-strand3069-3074618
α-helix3075-30773
α-helix3082-309312
α-helix3103-311816
α-helix3126-313813
β-strand3143-3147518
α-helix3156-31594
α-helix3164-31663
β-strand3169118
β-strand3174119
α-helix3178-31869
α-helix3203-32097
α-helix3223-324826
α-helix3257-332165
α-helix3323-333412
α-helix3336-33394
α-helix3342-33465
α-helix3350-33545
α-helix3356-336510
α-helix3366-33683
α-helix3372-338110
α-helix3385-33939
α-helix3399-341113
α-helix3419-34246
α-helix3425-34273
α-helix3431-34366
α-helix3445-34495
α-helix3450-34523
α-helix3453-34575
α-helix3464-34707
α-helix3474-348815
α-helix3515-35173
α-helix3518-353215
α-helix3536-359863
α-helix3602-36043
α-helix3607-362418
α-helix3634-36374
α-helix3641-36499
α-helix3656-36649
β-strand3672-3675420
α-helix3680-36889
β-strand3698121
α-helix3703-371412
β-strand3717122
β-strand3720120
β-strand3721121
α-helix3723-37253
β-strand3761122
β-strand3764-3765220
α-helix3775-37795
β-strand3782-3785420
α-helix3790-380213
α-helix3808-383629
α-helix3845-38473
α-helix3850-386213
α-helix3864-38674
α-helix3869-388416
α-helix3887-390115
α-helix3903-39053
α-helix3913-392412
α-helix3936-395520
α-helix3961-397515
α-helix3982-39843
α-helix3988-39925
α-helix4006-40083
α-helix4014-402512
α-helix4028-40303
α-helix4033-40397
α-helix4041-40488
α-helix4060-40678
α-helix4075-408915
α-helix4094-410613
α-helix4118-41247
β-strand4132-4136523
α-helix4143-41519
β-strand4161124
α-helix4165-41673
α-helix4168-417710
α-helix4178-41825
β-strand4188124
α-helix4190-41923
α-helix4197-42048
β-strand4216-4220523
α-helix4227-42315
α-helix4244-425310
α-helix4257-42604
α-helix4267-428317
α-helix4284-42874
α-helix4300-431617
α-helix4326-43283
α-helix4331-43377
α-helix4339-43435
α-helix4344-43463
α-helix4350-436314
α-helix4366-43694
β-strand4374-4376325
β-strand4381-4382225
α-helix4389-43979
α-helix4414-443017
α-helix4458-44614
α-helix4496-451722
α-helix4518-45203
α-helix4533-45364
α-helix4540-45423
α-helix4548-45503
α-helix4561-458020
α-helix4591-45933
α-helix4597-460913
β-strand4636-4639426
β-strand4642-4645427
β-strand4648-4650328
β-strand4653-4655328
β-strand4661-4664427
β-strand4667-4670426
α-helix4681-46833
β-strand4686-4691627
β-strand4693129
β-strand4699-4705727
β-strand4707128
α-helix4713-47175
β-strand4722-4724327
β-strand4726129
Chain B: 139 helices, 77 β-strands
ElementResiduesLengthSheet
α-helix1479-14868
α-helix1499-15046
α-helix1511-153828
β-strand1542130
β-strand1544-1548531
β-strand1552-1556531
α-helix1558-157417
α-helix1581-161838
α-helix1630-165122
β-strand1655130
α-helix1656-16594
α-helix1665-169329
α-helix1695-16995
α-helix1702-17109
α-helix1715-17184
α-helix1719-17213
α-helix1722-17254
β-strand1729-1734632
β-strand1740-1746732
β-strand1751-1759932
α-helix1766-179328
α-helix1800-18078
α-helix1812-183120
α-helix1838-186023
α-helix1862-18643
α-helix1869-189426
α-helix1904-19074
β-strand1910-1914533
β-strand1925-1929533
β-strand1932-1935433
α-helix1951-196414
β-strand1969-1973534
α-helix1980-199011
β-strand1995-1999534
α-helix2006-201813
β-strand2022-2026534
α-helix2028-20303
α-helix2033-205119
β-strand2056135
β-strand2066135
β-strand2072-2075434
β-strand2077134
α-helix2089-20913
β-strand2095-2099534
α-helix2105-211612
α-helix2121-213818
α-helix2149-216315
α-helix2187-220216
α-helix2204-22063
α-helix2209-22113
α-helix2212-222211
α-helix2234-224411
α-helix2253-226513
β-strand2271-2273336
α-helix2282-229615
β-strand2300-2303437
β-strand2306136
α-helix2313-23175
β-strand2320138
β-strand2327138
α-helix2331-234010
α-helix2346-23483
β-strand2349-2352437
β-strand2353-2355336
α-helix2363-23653
α-helix2368-23714
β-strand2376-2377239
β-strand2385-2386239
β-strand2393-2395336
α-helix2405-24073
β-strand2412-2413236
α-helix2418-24203
α-helix2423-243614
α-helix2492-250110
α-helix2511-25199
β-strand2524140
α-helix2530-254920
α-helix2551-25544
α-helix2559-25613
α-helix2564-258017
β-strand2585140
α-helix2587-259812
α-helix2612-26143
β-strand2615-2617341
β-strand2624-2626341
α-helix2627-26293
α-helix2651-266313
β-strand2671-2673342
α-helix2680-268910
β-strand2694-2697442
β-strand2700142
α-helix2707-27126
β-strand2718-2723643
β-strand2727-2732643
β-strand2738-2744742
α-helix2758-276811
β-strand2771-2774443
β-strand2779-2783543
β-strand2786-2792742
α-helix2800-28045
α-helix2805-28084
β-strand2813142
α-helix2821-283515
α-helix2841-28433
α-helix2846-286318
α-helix2876-289116
α-helix2898-291316
α-helix2920-293718
β-strand2952-2953244
β-strand2961-2962244
α-helix2965-298218
α-helix2992-300514
β-strand3012145
β-strand3015-3016246
α-helix3022-303211
α-helix30351
β-strand3036-3038345
α-helix3048-306316
β-strand3069-3074645
α-helix3082-309211
α-helix3104-311714
α-helix3127-313711
β-strand3141-3146645
β-strand3147146
α-helix3156-31605
α-helix3164-31674
β-strand3172-3174346
α-helix3178-318710
α-helix3203-32097
α-helix3223-324927
α-helix3257-334185
α-helix3343-33464
α-helix3348-33558
α-helix3513-357563
α-helix3578-360023
α-helix3602-36043
α-helix3607-362418
α-helix3634-36374
α-helix3641-36488
α-helix3656-36649
β-strand3672-3675447
α-helix3680-36889
β-strand3695-3698447
α-helix3703-37108
α-helix3711-37155
β-strand3718-3721447
α-helix3723-37253
α-helix3728-37303
α-helix3731-37344
β-strand3762-3766547
α-helix3775-37784
β-strand3782-3785447
α-helix3790-380516
α-helix3807-383731
α-helix3850-390253
α-helix3903-39053
α-helix3913-392412
α-helix3928-39314
α-helix3936-395520
α-helix3963-397311
α-helix3982-39843
α-helix3985-39928
α-helix4006-40083
α-helix4014-402512
α-helix4028-40303
α-helix4033-40397
α-helix4041-40444
α-helix4060-40689
α-helix4075-408915
α-helix4094-410613
α-helix4114-41163
α-helix4118-41236
β-strand4132-4136548
α-helix4143-415210
β-strand4157-4161548
α-helix4166-418116
β-strand4184-4188548
α-helix4194-420512
β-strand4214-4220748
α-helix4227-42315
β-strand4234-4238548
α-helix4244-42529
α-helix4257-42604
α-helix4266-428318
α-helix4284-42863
α-helix4300-431617
α-helix4326-43283
α-helix4331-43377
α-helix4338-43425
α-helix4350-436314
α-helix4366-43694
β-strand4374-4376349
β-strand4381-4382249
α-helix4389-43968
α-helix4414-443219
α-helix4458-44625
α-helix4494-452128
α-helix4532-454312
α-helix4548-45503
α-helix4561-458020
β-strand4589150
α-helix4591-45933
α-helix4597-461216
β-strand4619151
β-strand4637-4639350
β-strand4643-4645352
β-strand4648-4649253
β-strand4654-4655253
β-strand4663152
β-strand4667-4669350
β-strand4673151
β-strand4686-4691652
β-strand4699-4705752
β-strand4707153
α-helix4713-47197
β-strand4722-4724352

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Dynein heavy chain, cytoplasmicA, Bprotein3367Dictyostelium discoideumP34036
Sequence of entity 1 (A, B), FASTA
>3VKH_1 Dynein heavy chain, cytoplasmic (chains A, B)
MTRHHHHHHGGGDYKDDDDKGGGKVPVEEEIQDLKAVWVELSNTWQEIDSLKETAWSAII
PRKVRKSLEDTLQKLKNLPNRIRQYSAFDHAQNLIKIYLKGNAIITDLHSEAIKDRHWKI
LKKRLNTNWIITELTLGSIWDSDLARNENIYREVITAAQGEIALEEFLKGVREFWTTLEL
DLVNYQRKCKLVRGWDDLFNKLAEHLNSISAMKMSPYYKVFEEEANHWDDRLNKVRSLLD
VWIDVQRRWVYLEGIFSGSGDINQLLPAESTRFKSINSEFIAILKKVSGAPLILEVLAIE
RIQQTMERLSDLLGKVQKALGEYLERQRSAFARFYFVGDEDLLEIIGNSKDIIKIQKHFR
KMFAGLANLTLDDEKTTIIGMSSAEGETVTFKKPISIANGPKIHEWLTMVESEMKSTLAT
LLSESLQHFNQVDVNDHSKYSEWVDNYPTQLVLLTSQIVWSTQVDQALGGGTLQQSKIQE
QLQSIEQTTQMILNNLADSVLQDLSAQKRKKFEHLITELVHQRDVVRQLQKCKNLTGNKD
FDWLYHMRYYYDATQENVLHKLVIHMANATFYYGFEYLGIGERLVQTPLTDRCYLTLTQA
LESRMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWG
CFDEFNRLEERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAG
RSNLPDNLKKLFRSMAMIKPDREMIAQVMLYSQGFKTAEVLAGKIVPLFKLCQEQLSAQS
HYDFGLRALKSVLVSAGGIKRKCQPPQLPPITDAESKTKADQIYCQYEIGVLLNSINDTM
IPKLVADDIPLIQSLLLDVFPGSQLQPIQMDQLRKKIQEIAKQRHLVTKQEWVEKILQLH
QILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDNIKSEAHVMDPKAITKDQLFGSLDLT
TREWTDGLFTATLRRIIDNVRGESTKRHWIIFDGDVDPEWVENLNSLLDDNKLLTLPNGE
RLALPNNVRVMFEVQDLKYATLATISRCGMVWFSEEILTTQMIFQNYLDTLSNEPFDPQE
KEQQKRNENAQLQQQQQTTITSPILTSPPTTSSSSRSTTSTTSMIPAGLKVQKECAAIIS
QYFEPGGLVHKVLEDAGQRPHIMDFTRLRVLNSFFSLMNRSIVNVIEYNQLHSDFPMSPE
NQSNYITNRLLYSLMWGLGGSMGLVERENFSKFIQTIAITPVPANTIPLLDYSVSIDDAN
WSLWKNKVPSVEVETHKVASPDVVIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMT
LTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFC
DEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQL
THRFLRHAPILLVDFPSTSSLTQIYGTFNRALMKLLPNLRSFADNLTDAMVEFYSESQKR
FTPDIQAHYIYSPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLFQDRLVETEEK
EWTDKKIDEVALKHFPSVNLDALKRPILYSNWLTKDYQPVNRSDLREYVKARLKVFYEEE
LDVPLVLFNEVLDHILRIDRVFRQPQGHALLIGVSGGGKSVLSRFVAWMNGLSIYTIKVN
NNYKSSDFDDDLRMLLKRAGCKEEKICFIFDESNVLESSFLERMNTLLAGGEVPGLFEGE
EFTALMHACKETAQRNGLILDSEEELYKYFTSQVRRNLHVVFTMNPASPDFHNRSATSPA
LFNRCVLDWFGEWSPEALFQVGSEFTRNLDLENPQYIAPPVFIQEAEIMGNNLMAIPPSH
RDAVVSSLVYIHQTIGEANIRLLKRQGRQNYVTPRHYLDFINQVVLLINEKRDQLEEEQL
HLNIGLKKLRDTEAQVKDLQVSLAQKNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARE
LQVQLDVRNKEIAVQKVKAYADLEKAEPAIIEAQEAVSTIKKKHLDEIKSLPKPPTPVKL
AMEAVCLMLGGKKLEWADIRKKIMEPNFITSIINYDTKKMMTPKIREAITKGYLEDPGFD
YETVNRASKACGPLVKWATAQTYYSEILDRIKPLREEVEQLENAANELKLKQDEIVATIT
ALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFNT
QMSTVVGDVVLASAFLAYIGFFDQNFRTDLMRKWMIRLDSVGIKFKSDLSVPSFLSKPEE
RLNWHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLMNQYADKKITKTSFLDSS
FMKNLESALRFGCPLLVQDVENIDPVLNPVLNKEIRKKGGRILIRLGDQDVDFSPSFMIF
LFTRDPTAHFTPDLCSRVTFVNFTVTPSSLQSQCLHEALKTERPDTHKKRSDLLKIQGEF
QVKLRILEKSLLNALSQASGNILDDDSVISTLETLKKETTEIALKVEETETVMQEISEVS
ALYNPMALSCSRVYFAMEELSQFHLYQFSLRAFLDIFYNLLNNNPNLVDKKDPNERLVYL
SKDIFSMTFNRVTRTLLNDDKLTFALQLTIISVKGTSNEIEESEWDFLLKGGDNLTSIKE
TIPQLDSLLSTTQQKWLICLRQQVPSFSKLVDHIQQNSSDWKQFFGKDQVGEPIIPESWI
VAQAQLSNQQSTIVSNFRKILLMKAFHSDRVLQYSHSFVCSVFGEDFLNTQELDMANIVE
KEVKSSSPLLLCSVPGYDASSKVDDLALQLHKQYKSFAIGSPEGFELAEKSIYAAAKSGT
WVLLKNIHLAPQWLVQLEKKLHSLSPHPSFRLFMTSEIHPALPANLLRMSNVFSYENPPG
VKANLLHTFIGIPATRMDKQPAERSRIYFLLAWFHAIIQERLRYIPLGWTKFFEFNDADL
RGALDSIDYWVDLYSKGRSNIDPDKIPWIAVRTILGSTIYGGRIDNEFDMRLLYSFLEQL
FTPSAFNPDFPLVPSIGLSVPEGTTRAHFMKWIEALPEISTPIWLGLPENAESLLLSNKA
RKMINDLQKMQSSEEDGEDDQVSGSSKKESSSSSSEDKGKAKLRATITEWTKLLPKPLKQ
LKRTTQNIKDPLFRCFEREISTGGKLVKKITNDLANLLELISGNIKSTNYLRSLTTSISK
GIVPKEWKWYSVPETISLSVWISDFSKRMQQLSEISESSDYSSIQVWLGGLLNPEAYITA
TRQSASQLNGWSLENLRLHASSLGKISSEGGASFNVKGMALEGAVWNNDQLTPTDILSTP
ISIATLTWKDKDDPIFNNSSSKLSVPVYLNETRSELLFSIDLPYDQSTSKQNWYQRSVSI
SSWKSDI

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P28

Primary citation

The 2.8 A crystal structure of the dynein motor domain. Kon, T., Oyama, T., Shimo-Kon, R. et al. Nature (2012) 484:345-350. DOI 10.1038/nature10955 · PubMed

Other PDB entries of the same protein (UniProt P34036), best resolution first:

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