3VKG: MTBD truncation mutant of dynein motor domain

X-ray structure of an MTBD truncation mutant of dynein motor domain. Determined by X-ray diffraction at 2.81 Å resolution. Released 14 Mar 2012.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Dictyostelium discoideum
Chains: 2
Atoms: 45,284
Mol. weight: 745.15 kDa
Ligands: MG, SPM, ADP
Released: 14 Mar 2012

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

Secondary structure: helices and β-sheets

3VKG contains 291 α-helices and 141 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: 146 helices, 72 β-strands

Element	Residues	Length	Sheet
α-helix	1411-1416	6
α-helix	1451-1464	14
α-helix	1466-1470	5
α-helix	1478-1487	10
α-helix	1499-1504	6
α-helix	1507-1540	34
β-strand	1542	1	1
β-strand	1544-1548	5	2
β-strand	1552-1556	5	2
α-helix	1558-1574	17
α-helix	1583-1586	4
α-helix	1587-1618	32
α-helix	1630-1652	23
β-strand	1655	1	1
α-helix	1656-1659	4
α-helix	1665-1692	28
α-helix	1695-1699	5
α-helix	1702-1710	9
α-helix	1711-1713	3
α-helix	1715-1717	3
α-helix	1719-1724	6
β-strand	1731-1734	4	3
β-strand	1740-1745	6	3
β-strand	1751-1759	9	3
α-helix	1766-1792	27
α-helix	1800-1808	9
α-helix	1812-1831	20
α-helix	1838-1862	25
α-helix	1869-1893	25
α-helix	1904-1907	4
β-strand	1910-1914	5	4
α-helix	1922-1924	3
β-strand	1925-1929	5	4
β-strand	1932-1935	4	4
α-helix	1951-1965	15
β-strand	1969-1973	5	5
α-helix	1980-1990	11
β-strand	1995-1999	5	5
α-helix	2006-2019	14
β-strand	2022-2026	5	5
α-helix	2033-2052	20
β-strand	2056-2057	2	6
β-strand	2065-2066	2	6
β-strand	2072-2075	4	5
β-strand	2077	1	5
α-helix	2081-2083	3
α-helix	2089-2092	4
β-strand	2095-2099	5	5
α-helix	2105-2114	10
α-helix	2121-2137	17
α-helix	2149-2164	16
α-helix	2177-2201	25
α-helix	2209-2211	3
α-helix	2212-2222	11
α-helix	2228-2231	4
α-helix	2234-2246	13
α-helix	2253-2266	14
β-strand	2271-2275	5	7
α-helix	2282-2293	12
β-strand	2300-2306	7	7
α-helix	2313-2317	5
β-strand	2318-2320	3	8
β-strand	2327-2329	3	8
α-helix	2331-2340	10
α-helix	2346-2348	3
β-strand	2349-2356	8	7
α-helix	2361-2364	4
α-helix	2368-2371	4
β-strand	2376-2377	2	9
β-strand	2385-2386	2	9
β-strand	2391-2397	7	7
α-helix	2405-2409	5
β-strand	2412-2415	4	7
α-helix	2423-2434	12
α-helix	2441-2451	11
α-helix	2490-2506	17
α-helix	2511-2520	10
α-helix	2530-2554	25
α-helix	2559-2561	3
α-helix	2562-2582	21
α-helix	2587-2598	12
α-helix	2612-2614	3
β-strand	2615-2617	3	10
β-strand	2624-2626	3	10
α-helix	2651-2665	15
β-strand	2671-2673	3	11
α-helix	2680-2687	8
α-helix	2688-2690	3
β-strand	2694-2699	6	11
α-helix	2707-2717	11
β-strand	2718-2722	5	12
β-strand	2728-2732	5	12
β-strand	2738-2743	6	11
α-helix	2758-2769	12
β-strand	2771-2774	4	12
β-strand	2779-2783	5	12
β-strand	2786-2792	7	11
α-helix	2800-2803	4
α-helix	2805-2808	4
β-strand	2813-2815	3	11
α-helix	2818-2820	3
α-helix	2821-2835	15
α-helix	2840-2842	3
α-helix	2846-2863	18
α-helix	2876-2891	16
α-helix	2900-2913	14
α-helix	2920-2937	18
α-helix	2943-2946	4
α-helix	2947	1
α-helix	2965-2977	13
α-helix	2992-3005	14
β-strand	3012-3016	5	13
α-helix	3022-3032	11
β-strand	3036-3038	3	13
α-helix	3048-3063	16
β-strand	3069-3074	6	13
α-helix	3075-3077	3
α-helix	3082-3093	12
α-helix	3105-3118	14
α-helix	3126-3137	12
β-strand	3143-3147	5	13
α-helix	3163-3167	5
β-strand	3169-3174	6	13
α-helix	3178-3188	11
α-helix	3203-3210	8
α-helix	3223-3247	25
α-helix	3257-3364	108
α-helix	3497-3600	104
α-helix	3602-3604	3
α-helix	3607-3624	18
α-helix	3634-3637	4
α-helix	3641-3649	9
α-helix	3656-3664	9
β-strand	3672-3675	4	14
α-helix	3680-3688	9
α-helix	3690-3692	3
α-helix	3705-3714	10
β-strand	3718-3719	2	15
β-strand	3762-3763	2	15
β-strand	3764-3766	3	14
α-helix	3775-3779	5
β-strand	3782-3785	4	14
α-helix	3790-3805	16
α-helix	3807-3818	12
α-helix	3821-3828	8
α-helix	3832-3839	8
α-helix	3845-3847	3
α-helix	3849-3885	37
α-helix	3887-3900	14
α-helix	3902-3905	4
α-helix	3913-3924	12
α-helix	3928-3930	3
α-helix	3936-3955	20
α-helix	3961-3963	3
α-helix	3966-3975	10
α-helix	3982-3984	3
α-helix	3985-3993	9
α-helix	3998-4000	3
α-helix	4006-4008	3
α-helix	4014-4026	13
α-helix	4028-4030	3
α-helix	4033-4039	7
α-helix	4041-4047	7
α-helix	4062-4069	8
α-helix	4075-4089	15
α-helix	4091-4093	3
α-helix	4094-4105	12
α-helix	4118-4124	7
β-strand	4132-4133	2	16
β-strand	4135-4136	2	17
α-helix	4143-4153	11
β-strand	4161	1	18
β-strand	4162	1	19
β-strand	4164	1	19
α-helix	4165-4181	17
β-strand	4184-4186	3	16
β-strand	4188	1	18
α-helix	4190-4192	3
α-helix	4197-4205	9
β-strand	4214-4216	3	16
β-strand	4219-4220	2	17
α-helix	4227-4231	5
β-strand	4234-4235	2	16
β-strand	4238	1	17
α-helix	4244-4252	9
α-helix	4257-4260	4
α-helix	4266-4283	18
α-helix	4284-4287	4
α-helix	4300-4317	18
α-helix	4331-4336	6
α-helix	4337-4343	7
α-helix	4352-4363	12
α-helix	4366-4369	4
β-strand	4374-4376	3	20
α-helix	4377-4379	3
β-strand	4381-4382	2	20
α-helix	4383-4385	3
α-helix	4389-4396	8
α-helix	4405-4408	4
α-helix	4414-4435	22
α-helix	4456-4464	9
α-helix	4496-4520	25
α-helix	4561-4580	20
α-helix	4591-4593	3
α-helix	4597-4611	15
β-strand	4623	1	21
β-strand	4637-4639	3	21
β-strand	4643-4645	3	22
β-strand	4648-4649	2	23
β-strand	4654-4655	2	23
β-strand	4661-4663	3	22
β-strand	4667-4669	3	21
α-helix	4682-4684	3
β-strand	4685-4691	7	22
β-strand	4699-4706	8	22
β-strand	4707	1	23
α-helix	4713-4717	5
β-strand	4722-4724	3	22

Chain B: 145 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	1546-1548	3	24
β-strand	1552-1554	3	24
α-helix	1558-1570	13
α-helix	1591-1618	28
α-helix	1625-1628	4
α-helix	1630-1649	20
α-helix	1656-1660	5
α-helix	1665-1693	29
α-helix	1695-1699	5
α-helix	1702-1710	9
α-helix	1715-1719	5
α-helix	1722-1725	4
β-strand	1731-1734	4	25
β-strand	1740-1745	6	25
β-strand	1751-1759	9	25
α-helix	1760-1762	3
α-helix	1766-1793	28
α-helix	1800-1807	8
α-helix	1812-1831	20
α-helix	1838-1860	23
α-helix	1869-1893	25
α-helix	1904-1907	4
β-strand	1910-1913	4	26
α-helix	1921-1923	3
β-strand	1926-1929	4	26
β-strand	1932-1934	3	26
α-helix	1951-1965	15
β-strand	1969-1973	5	27
α-helix	1980-1990	11
β-strand	1995-1999	5	27
α-helix	2006-2019	14
β-strand	2022-2026	5	27
α-helix	2028-2030	3
α-helix	2033-2051	19
β-strand	2056	1	28
β-strand	2066	1	28
β-strand	2072-2077	6	27
α-helix	2081-2083	3
α-helix	2089-2092	4
β-strand	2095-2099	5	27
α-helix	2105-2116	12
α-helix	2121-2138	18
α-helix	2149-2163	15
α-helix	2177-2202	26
α-helix	2204-2206	3
α-helix	2209-2211	3
α-helix	2212-2222	11
α-helix	2234-2246	13
α-helix	2253-2268	16
β-strand	2271-2275	5	29
α-helix	2282-2297	16
β-strand	2301-2306	6	29
α-helix	2313-2317	5
β-strand	2318-2320	3	30
β-strand	2327-2329	3	30
α-helix	2331-2340	10
β-strand	2350-2355	6	29
α-helix	2361-2365	5
α-helix	2368-2371	4
β-strand	2376-2377	2	31
β-strand	2385-2386	2	31
β-strand	2391-2397	7	29
α-helix	2405-2407	3
β-strand	2412-2415	4	29
α-helix	2418-2420	3
α-helix	2423-2436	14
α-helix	2493-2503	11
α-helix	2504-2506	3
α-helix	2511-2519	9
α-helix	2530-2555	26
α-helix	2564-2582	19
α-helix	2587-2598	12
α-helix	2612-2614	3
β-strand	2615-2617	3	32
β-strand	2624-2626	3	32
α-helix	2627-2629	3
α-helix	2638-2640	3
α-helix	2651-2665	15
β-strand	2671-2673	3	33
α-helix	2680-2687	8
β-strand	2694-2700	7	33
α-helix	2707-2712	6
β-strand	2718-2723	6	34
β-strand	2727-2732	6	34
β-strand	2738-2744	7	33
α-helix	2758-2764	7
α-helix	2765-2769	5
β-strand	2771-2774	4	34
β-strand	2779-2783	5	34
β-strand	2786-2792	7	33
α-helix	2800-2804	5
α-helix	2805-2808	4
β-strand	2813-2815	3	33
α-helix	2818-2820	3
α-helix	2821-2835	15
α-helix	2840-2845	6
α-helix	2846-2863	18
α-helix	2876-2890	15
α-helix	2898-2913	16
α-helix	2920-2937	18
α-helix	2943-2946	4
α-helix	2947	1
β-strand	2952	1	35
β-strand	2962	1	35
α-helix	2965-2981	17
α-helix	2992-3005	14
β-strand	3012-3016	5	36
α-helix	3022-3032	11
α-helix	3035	1
β-strand	3036-3038	3	36
α-helix	3051-3063	13
β-strand	3069-3074	6	36
α-helix	3082-3091	10
α-helix	3104-3106	3
α-helix	3107-3117	11
α-helix	3126-3134	9
β-strand	3141-3147	7	36
α-helix	3155-3160	6
α-helix	3164-3167	4
β-strand	3169-3174	6	36
α-helix	3178-3187	10
α-helix	3203-3210	8
α-helix	3223-3249	27
α-helix	3257-3355	99
α-helix	3508-3575	68
α-helix	3580-3585	6
α-helix	3588-3600	13
α-helix	3602-3604	3
α-helix	3607-3624	18
α-helix	3635-3638	4
α-helix	3641-3649	9
α-helix	3656-3667	12
α-helix	3671	1
β-strand	3672-3675	4	37
α-helix	3680-3690	11
β-strand	3695-3698	4	37
α-helix	3703-3713	11
β-strand	3717-3721	5	37
α-helix	3723-3725	3
α-helix	3731-3734	4
β-strand	3761-3766	6	37
α-helix	3775-3780	6
β-strand	3782-3785	4	37
α-helix	3790-3805	16
α-helix	3807-3822	16
α-helix	3826-3838	13
α-helix	3843-3846	4
α-helix	3850-3863	14
α-helix	3865-3900	36
α-helix	3903-3905	3
α-helix	3913-3924	12
α-helix	3928-3930	3
α-helix	3936-3955	20
α-helix	3963-3975	13
α-helix	3985-3993	9
α-helix	4006-4010	5
α-helix	4014-4026	13
α-helix	4033-4039	7
α-helix	4041-4048	8
α-helix	4060-4068	9
α-helix	4075-4089	15
α-helix	4091-4093	3
α-helix	4094-4103	10
α-helix	4114-4116	3
α-helix	4118-4124	7
β-strand	4132-4136	5	38
α-helix	4143-4153	11
β-strand	4157-4161	5	38
β-strand	4162	1	39
β-strand	4164	1	39
α-helix	4165-4181	17
β-strand	4184-4188	5	38
α-helix	4190-4192	3
α-helix	4194-4205	12
β-strand	4214-4220	7	38
α-helix	4227-4231	5
β-strand	4234-4238	5	38
α-helix	4240-4242	3
α-helix	4244-4253	10
α-helix	4257-4260	4
α-helix	4262	1
α-helix	4266-4283	18
α-helix	4284-4287	4
α-helix	4300-4317	18
α-helix	4326-4328	3
α-helix	4331-4337	7
α-helix	4338-4343	6
α-helix	4350-4363	14
α-helix	4367-4369	3
β-strand	4374-4376	3	40
β-strand	4381-4382	2	40
α-helix	4389-4397	9
α-helix	4405-4408	4
α-helix	4414-4435	22
α-helix	4457-4463	7
α-helix	4494-4522	29
α-helix	4532-4543	12
α-helix	4561-4579	19
β-strand	4589	1	41
α-helix	4591-4593	3
α-helix	4597-4610	14
β-strand	4619-4620	2	42
β-strand	4637-4639	3	41
β-strand	4642-4645	4	43
β-strand	4648-4650	3	44
β-strand	4653-4655	3	44
β-strand	4661-4664	4	43
β-strand	4667-4669	3	41
β-strand	4672-4673	2	42
β-strand	4686-4691	6	43
β-strand	4699-4705	7	43
β-strand	4707	1	44
α-helix	4713-4717	5
β-strand	4722-4724	3	43

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dynein heavy chain, cytoplasmic	A, B	protein	3245	Dictyostelium discoideum	P34036

Sequence of entity 1 (A, B), FASTA

>3VKG_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
LQVQLDVRNKEIAVQKVKAYADLEKAEPTGPLREEVEQLENAANELKLKQDEIVATITAL
EKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFNTQM
STVVGDVVLASAFLAYIGFFDQNFRTDLMRKWMIRLDSVGIKFKSDLSVPSFLSKPEERL
NWHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLMNQYADKKITKTSFLDSSFM
KNLESALRFGCPLLVQDVENIDPVLNPVLNKEIRKKGGRILIRLGDQDVDFSPSFMIFLF
TRDPTAHFTPDLCSRVTFVNFTVTPSSLQSQCLHEALKTERPDTHKKRSDLLKIQGEFQV
KLRILEKSLLNALSQASGNILDDDSVISTLETLKKETTEIALKVEETETVMQEISEVSAL
YNPMALSCSRVYFAMEELSQFHLYQFSLRAFLDIFYNLLNNNPNLVDKKDPNERLVYLSK
DIFSMTFNRVTRTLLNDDKLTFALQLTIISVKGTSNEIEESEWDFLLKGGDNLTSIKETI
PQLDSLLSTTQQKWLICLRQQVPSFSKLVDHIQQNSSDWKQFFGKDQVGEPIIPESWIVA
QAQLSNQQSTIVSNFRKILLMKAFHSDRVLQYSHSFVCSVFGEDFLNTQELDMANIVEKE
VKSSSPLLLCSVPGYDASSKVDDLALQLHKQYKSFAIGSPEGFELAEKSIYAAAKSGTWV
LLKNIHLAPQWLVQLEKKLHSLSPHPSFRLFMTSEIHPALPANLLRMSNVFSYENPPGVK
ANLLHTFIGIPATRMDKQPAERSRIYFLLAWFHAIIQERLRYIPLGWTKFFEFNDADLRG
ALDSIDYWVDLYSKGRSNIDPDKIPWIAVRTILGSTIYGGRIDNEFDMRLLYSFLEQLFT
PSAFNPDFPLVPSIGLSVPEGTTRAHFMKWIEALPEISTPIWLGLPENAESLLLSNKARK
MINDLQKMQSSEEDGEDDQVSGSSKKESSSSSSEDKGKAKLRATITEWTKLLPKPLKQLK
RTTQNIKDPLFRCFEREISTGGKLVKKITNDLANLLELISGNIKSTNYLRSLTTSISKGI
VPKEWKWYSVPETISLSVWISDFSKRMQQLSEISESSDYSSIQVWLGGLLNPEAYITATR
QSASQLNGWSLENLRLHASSLGKISSEGGASFNVKGMALEGAVWNNDQLTPTDILSTPIS
IATLTWKDKDDPIFNNSSSKLSVPVYLNETRSELLFSIDLPYDQSTSKQNWYQRSVSISS
WKSDI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
SPM	Spermine	C10 H26 N4	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	8

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:

27PT 2.2 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in complex with ADP.Vi…
27PY 2.61 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (ADP…
27QB 2.66 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide…
27QA 2.76 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (Apo…
27PZ 3.2 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (ADP…
3VKH 3.8 Å, X-ray structure of a functional full-length dynein motor domain
3J6P 8.2 Å, Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a…

Browse structure collections

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