6DJX: PParkin-pUb-UbcH7 complex

Crystal Structure of pParkin-pUb-UbcH7 complex. Determined by X-ray diffraction at 4.8 Å resolution. Released 4 Jul 2018.

Method: X-ray diffraction
Resolution: 4.8 Å
Organisms: Bactrocera dorsalis, Bos taurus, Homo sapiens
Chains: 3
Atoms: 4,346
Mol. weight: 76.12 kDa
Ligands: ZN
Released: 4 Jul 2018

Explore 6DJX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DJX contains 18 α-helices and 42 β-strands across 3 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: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	1
β-strand	41-46	6	1
β-strand	51	1	2
α-helix	52-63	12
β-strand	70-74	5	3
β-strand	77-78	2	3
β-strand	84	1	2
α-helix	86-88	3
β-strand	94-96	3	1
β-strand	97-100	4	3
β-strand	175-176	2	4
β-strand	184	1	4
β-strand	186-191	6	5
β-strand	200	1	6
β-strand	222	1	6
α-helix	224-227	4
β-strand	241-246	6	5
β-strand	259-260	2	4
β-strand	264-266	3	7
α-helix	271	1
β-strand	272	1	8
α-helix	273	1
β-strand	279	1	8
β-strand	282-285	4	7
β-strand	293-295	3	7
α-helix	296-307	12
α-helix	312	1
β-strand	313-315	3	9
β-strand	319-321	3	9
α-helix	336-341	6
α-helix	344-361	18
β-strand	365	1	10
β-strand	376-377	2	10
β-strand	395	1	11
β-strand	402	1	11

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	12-16	5	10
β-strand	22	1	12
α-helix	23-34	12
β-strand	41-45	5	10
β-strand	48-49	2	10
α-helix	50-51	2
β-strand	55	1	12
α-helix	57-59	3
β-strand	66-72	7	10

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	22-26	5	13
β-strand	34-39	6	13
α-helix	44-46	3
β-strand	49-50	2	14
β-strand	51-56	6	13
α-helix	61-63	3
β-strand	67-70	4	13
β-strand	79	1	15
β-strand	84	1	13
β-strand	85	1	15
α-helix	101-113	13
α-helix	123-131	9
α-helix	134-146	13
β-strand	149-150	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RBR-type E3 ubiquitin transferase,RBR-type E3 ubiquitin transferase	A	protein	432	Bactrocera dorsalis	A0A034W4L8 (AlphaFold model)
Ubiquitin	B	protein	76	Bos taurus	P62992 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	C	protein	159	Homo sapiens	P68036 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6DJX_1 RBR-type E3 ubiquitin transferase,RBR-type E3 ubiquitin transferase (chains A)
GGENLYLGGSLSIYIKTNTGRTLSVNLEPQWDIKNVKEIVAPQLGLQPEEVKIIFAGKEL
SDATTIQECDLGQQSILHAIRSRPQPQRQRSEERINITEEDRQRTKAHFFVHCAQCNKLC
KGKLRVRCSLCKGGAFTVHRDPECWDDVLKPRRITGHCESQEIACFDNETGDPPFTEFYF
KCGEHVSGGEKDFAAPLNLIKINIKDVPCLACTEVSETVLVFPCESKHVTCLECFEQYCR
SRLSERQFMPHPDIGYTLPCPAGCENSFIEEIHHFKLLSREEYARYQRFATEEYVLQAGG
VLCPQPGCGMGLLVEPECKKVTCQNGCGYVFCRNCLQGYHLGDCLPEGTSTNASGSCEYS
VDPNRAAEARWDEASKVTIKVMTKPCPKCRTPTERDGGAMHMVCTRAGCGFEWCWICQTE
WTRDCMGAHWFG

Sequence of entity 2 (B), FASTA

>6DJX_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>6DJX_3 Ubiquitin-conjugating enzyme E2 L3 (chains C)
GPLGSMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEI
NFPAEYPFKPPKITFKTKIYHPNIDEKGQVKLPVISAENWKPATKTDQVIQSLIALVNDP
QPEHPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Mechanism of parkin activation by phosphorylation. Sauve, V., Sung, G., Soya, N. et al. Nat Struct Mol Biol (2018) 25:623-630. DOI 10.1038/s41594-018-0088-7 · PubMed

Other PDB entries of the same protein (UniProt A0A034W4L8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DJW 3.8 Å, Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex

Browse structure collections

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