6IIK: USP14 catalytic domain with IU1

USP14 catalytic domain with IU1. Determined by X-ray diffraction at 1.97 Å resolution. Released 12 Dec 2018.

Method: X-ray diffraction
Resolution: 1.97 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,754
Mol. weight: 91.81 kDa
Ligands: IU1
Released: 12 Dec 2018

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

Secondary structure: helices and β-sheets

6IIK contains 36 α-helices and 48 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: 19 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	103-105	3
β-strand	106-107	2	1
α-helix	114-124	11
α-helix	127-135	9
α-helix	147-165	19
β-strand	169-170	2	1
α-helix	173-182	10
α-helix	184-187	4
β-strand	189	1	2
α-helix	194	1
β-strand	195	1	2
α-helix	196-197	2
α-helix	200-214	15
β-strand	216	1	3
α-helix	217-219	3
β-strand	241	1	3
α-helix	242-247	6
β-strand	249-257	9	4
α-helix	264-265	2
β-strand	266-272	7	4
β-strand	275-278	4	5
β-strand	285	1	6
α-helix	286-293	8
β-strand	295-302	8	4
β-strand	307-319	13	4
β-strand	321	1	7
β-strand	324-329	6	5
α-helix	341-343	3
β-strand	348	1	6
β-strand	352-354	3	5
α-helix	356-358	3
β-strand	359	1	4
α-helix	361-376	16
β-strand	412	1	7
β-strand	417-427	11	5
β-strand	435-443	9	5
β-strand	446-451	6	5
β-strand	454-458	5	5
α-helix	460-464	5
α-helix	465-467	3
β-strand	474-482	9	5
α-helix	483-484	2

Chain B: 17 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	106-107	2	8
α-helix	114-124	11
α-helix	127-135	9
α-helix	147-165	19
β-strand	169-170	2	8
α-helix	173-182	10
α-helix	184-187	4
β-strand	189	1	9
α-helix	194	1
β-strand	195	1	9
α-helix	196-197	2
α-helix	200-214	15
β-strand	216	1	10
α-helix	217-218	2
β-strand	241	1	10
α-helix	242-247	6
β-strand	249-257	9	11
β-strand	266-272	7	11
β-strand	275-278	4	12
β-strand	285	1	13
α-helix	286-293	8
β-strand	295-301	7	11
β-strand	308-319	12	11
β-strand	321	1	14
β-strand	324-329	6	12
β-strand	348	1	13
β-strand	352-354	3	12
α-helix	356-358	3
β-strand	359	1	11
α-helix	361-371	11
α-helix	401-403	3
β-strand	406	1	15
β-strand	409	1	15
β-strand	412	1	14
β-strand	417-427	11	12
β-strand	435-443	9	12
β-strand	446-451	6	12
β-strand	454-458	5	12
α-helix	460-464	5
α-helix	465-467	3
β-strand	474-482	9	12
α-helix	483-484	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 14	A, B	protein	399	Homo sapiens	P54578 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6IIK_1 Ubiquitin carboxyl-terminal hydrolase 14 (chains A, B)
QLASAMELPCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAA
LRDLFDSMDKTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKL
EAIEDDSVKETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQL
SCFINQEVKYLFTGLKLRLQEEITKQSPTLQRNALYIKSSKISRLPAYLTIQMVRFFYKE
KESVNAKVLKDVKFPLMLDMYELCTPELQEKMVSFRSKFKDLEDKKVNQQPNTSDKKSSP
QKEVKYEPFSFADDIGSNNCGYYDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKV
SIVTPEDILRLSGGGDWHIAYVLLYGPRRVEIMEEESEQ

Ligands and cofactors

ID	Name	Formula	Copies
IU1	1-[1-(4-fluorophenyl)-2,5-dimethyl-1H-pyrrol-3-yl]-2-(pyrrolidin-1-yl)ethan-1-o…	C18 H21 F N2 O	2

Primary citation

Small molecule inhibitors reveal allosteric regulation of USP14 via steric blockade. Wang, Y., Jiang, Y., Ding, S. et al. Cell Res (2018) 28:1186-1194. DOI 10.1038/s41422-018-0091-x · PubMed

Other PDB entries of the same protein (UniProt P54578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
6IIL 2.2 Å, USP14 catalytic domain bind to IU1-47
6IIM 2.21 Å, USP14 catalytic domain with IU1-206
6IIN 2.53 Å, USP14 catalytic domain with IU1-248
6LVS 2.73 Å, USP14 catalytic domain mutant C114S
9F19 2.75 Å, Human USP30 chimera in complex with NK036 inhibitor
7W37 3.0 Å, Structure of USP14-bound human 26S proteasome in state EA1_UBL
7W38 3.1 Å, Structure of USP14-bound human 26S proteasome in state EA2.0_UBL
2AYN 3.2 Å, Structure of USP14, a proteasome-associated deubiquitinating enzyme
7W39 3.2 Å, Structure of USP14-bound human 26S proteasome in state EA2.1_UBL
7W3G 3.2 Å, Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.0_USP14
7W3H 3.2 Å, Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.1_USP14

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