2Y6E: Ubiquitin carboxyl-terminal hydrolase 4

Name: PDB 2Y6E: Structure of the D1D2 domain of USP4, the conserved catalytic domain
Published: 2011-04-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Structure of the D1D2 domain of USP4, the conserved catalytic domain. Determined by X-ray diffraction at 2.4 Å resolution. Released 6 Apr 2011.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 17,209
Mol. weight: 254.46 kDa
Ligands: ZN
Released: 6 Apr 2011

Explore 2Y6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Y6E contains 96 α-helices and 124 β-strands across 6 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: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	303-304	2	1
α-helix	311-321	11
α-helix	324-331	8
α-helix	335-338	4
α-helix	350-362	13
β-strand	369-370	2	1
α-helix	373-382	10
α-helix	384-386	3
α-helix	394-408	15
α-helix	419-421	3
α-helix	428-442	15
α-helix	446-451	6
β-strand	453-460	8	2
β-strand	467-474	8	2
β-strand	477-480	4	3
α-helix	481-482	2
β-strand	776-777	2	4
α-helix	778-785	8
β-strand	789-790	2	2
α-helix	796	1
β-strand	797-799	3	5
β-strand	804-806	3	5
β-strand	809-816	8	2
β-strand	820-826	7	3
β-strand	828-830	3	6
β-strand	835-837	3	6
α-helix	840-841	2
β-strand	842-843	2	4
β-strand	849-850	2	3
α-helix	852-854	3
β-strand	855	1	2
α-helix	861-862	2
β-strand	864-874	11	3
β-strand	881-887	7	3
β-strand	894-898	5	3
β-strand	901-904	4	3
α-helix	907-909	3
β-strand	915-922	8	3
α-helix	923-924	2

Chain B: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	297-298	2
β-strand	303-304	2	7
α-helix	311-321	11
α-helix	324-331	8
α-helix	336-338	3
α-helix	350-362	13
β-strand	369-370	2	7
α-helix	373-382	10
α-helix	384-387	4
α-helix	394-408	15
α-helix	428-440	13
α-helix	446-451	6
β-strand	453-460	8	8
β-strand	467-474	8	8
β-strand	477-480	4	9
α-helix	481-482	2
β-strand	776-777	2	10
α-helix	778-786	9
β-strand	789-790	2	8
β-strand	797-799	3	11
β-strand	804-806	3	11
β-strand	809-816	8	8
β-strand	820-826	7	9
β-strand	828-830	3	12
β-strand	835-837	3	12
α-helix	840-841	2
β-strand	842-843	2	10
β-strand	849-850	2	9
α-helix	852-854	3
β-strand	855	1	8
α-helix	861-862	2
β-strand	864-874	11	9
β-strand	881-887	7	9
β-strand	894-898	5	9
β-strand	901-904	4	9
α-helix	907-909	3
β-strand	915-922	8	9
α-helix	926-928	3

Chain C: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	297-298	2
β-strand	303-304	2	13
α-helix	311-321	11
α-helix	324-331	8
α-helix	335-338	4
α-helix	350-362	13
β-strand	369-370	2	13
α-helix	373-382	10
α-helix	384-386	3
α-helix	394-408	15
α-helix	428-442	15
α-helix	446-451	6
β-strand	453-460	8	14
β-strand	467-474	8	14
β-strand	477-480	4	15
α-helix	481-482	2
β-strand	776-777	2	16
α-helix	778-786	9
β-strand	789-790	2	14
β-strand	797-798	2	17
β-strand	805-806	2	17
β-strand	809-816	8	14
β-strand	820-826	7	15
β-strand	828-830	3	18
β-strand	835-837	3	18
α-helix	840-841	2
β-strand	842-843	2	16
β-strand	849-850	2	15
α-helix	852-854	3
β-strand	855	1	14
α-helix	861-862	2
β-strand	864-874	11	15
β-strand	878	1	19
β-strand	881-887	7	15
β-strand	894-898	5	15
β-strand	901-904	4	15
α-helix	907-909	3
β-strand	915-922	8	15

Chain D: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	303-304	2	20
β-strand	306	1	19
α-helix	311-321	11
α-helix	324-331	8
α-helix	335-338	4
α-helix	350-362	13
β-strand	369-370	2	20
α-helix	373-382	10
α-helix	384-386	3
α-helix	394-408	15
α-helix	428-442	15
α-helix	446-451	6
β-strand	453-459	7	21
β-strand	468-474	7	21
β-strand	477-479	3	22
α-helix	480-482	3
β-strand	775-777	3	23
α-helix	778-786	9
β-strand	789-790	2	24
β-strand	809-810	2	24
β-strand	811-816	6	21
β-strand	820-825	6	22
β-strand	828-830	3	25
β-strand	835-837	3	25
α-helix	840	1
β-strand	841-843	3	23
β-strand	849-850	2	22
α-helix	852-854	3
β-strand	855	1	21
α-helix	861-862	2
β-strand	864-874	11	22
β-strand	881-887	7	22
β-strand	894-898	5	22
β-strand	901-904	4	22
α-helix	907-909	3
β-strand	915-922	8	22

Chain E: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	303-304	2	26
α-helix	311-321	11
α-helix	324-331	8
α-helix	335-338	4
α-helix	350-362	13
β-strand	369-370	2	26
α-helix	373-382	10
α-helix	384-386	3
α-helix	394-408	15
α-helix	428-442	15
α-helix	446-451	6
β-strand	453-460	8	27
β-strand	467-474	8	27
β-strand	477-480	4	28
α-helix	481-482	2
β-strand	776-777	2	29
α-helix	778-786	9
β-strand	809-816	8	27
β-strand	820-826	7	28
β-strand	828-830	3	30
β-strand	835-837	3	30
α-helix	840-841	2
β-strand	842-843	2	29
β-strand	849-850	2	28
α-helix	852-854	3
β-strand	855	1	27
α-helix	861-862	2
β-strand	864-874	11	28
β-strand	878	1	31
β-strand	881-887	7	28
β-strand	894-898	5	28
β-strand	901-904	4	28
α-helix	907-909	3
β-strand	915-922	8	28

Chain F: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	297-298	2
β-strand	303-304	2	32
β-strand	306	1	31
α-helix	311-321	11
α-helix	324-331	8
α-helix	335-338	4
α-helix	350-362	13
β-strand	369-370	2	32
α-helix	373-382	10
α-helix	384-387	4
α-helix	394-408	15
α-helix	428-442	15
α-helix	446-451	6
β-strand	453-460	8	33
β-strand	467-474	8	33
β-strand	477-480	4	34
α-helix	481-482	2
β-strand	776-777	2	35
α-helix	778-786	9
α-helix	788	1
β-strand	789	1	33
β-strand	809-816	8	33
β-strand	820-826	7	34
β-strand	828-830	3	36
β-strand	835-837	3	36
β-strand	842-843	2	35
β-strand	849-850	2	34
β-strand	855	1	33
α-helix	861-862	2
β-strand	864-874	11	34
β-strand	881-887	7	34
β-strand	894-898	5	34
β-strand	901-904	4	34
α-helix	907-909	3
β-strand	915-922	8	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 4	A, B, C, D, E, F	protein	367	HOMO SAPIENS	Q13107 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>2Y6E_1 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4 (chains A, B, C, D, E, F)
GMHIQPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAE
AYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVK
KKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDP
FCYLTLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKH
QQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVY
DLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDD
EFYKTPS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

The Dusp-Ubl Domain of Usp4 Enhances its Catalytic Efficiency by Promoting Ubiquitin Exchange. Clerici, M., Luna-Vargas, M.P.A., Faesen, A.C. et al. Nat Commun (2014) 5:5399. DOI 10.1038/NCOMMS6399 · PubMed

Other PDB entries of the same protein (UniProt Q13107 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CTR 3.01 Å, Crystal structure of human SART3 HAT-C domain-human USP4 DUSP-UBL domain complex

Browse structure collections

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