6QML: UCHL3

UCHL3 in complex with synthetic, K27-linked diubiquitin. Determined by X-ray diffraction at 2.1 Å resolution. Released 26 Feb 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,397
Mol. weight: 87.58 kDa
Released: 26 Feb 2020

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

Secondary structure: helices and β-sheets

6QML contains 38 α-helices and 56 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: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
α-helix	6-8	3
β-strand	9-10	2	2
α-helix	13-22	10
β-strand	25	1	3
β-strand	29-33	5	4
α-helix	39-42	4
β-strand	49-57	9	4
α-helix	60-76	17
β-strand	92	1	1
α-helix	95-105	11
α-helix	108-110	3
β-strand	113	1	3
α-helix	118-126	9
α-helix	131-139	9
α-helix	142-152	11
β-strand	155	1	5
β-strand	168-176	9	4
β-strand	179-183	5	4
β-strand	191-195	5	4
α-helix	201-215	15
β-strand	223-229	7	4

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	6
β-strand	48-49	2	6
α-helix	50-51	2
β-strand	55	1	7
α-helix	57-59	3
β-strand	66-71	6	6
β-strand	74-75	2	2

Chains C and F: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	8
β-strand	48-49	2	8
α-helix	50-51	2
β-strand	55	1	9
α-helix	57-59	3
β-strand	66-71	6	8
β-strand	72	1	5

Chain D: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	10
α-helix	6-8	3
β-strand	9-10	2	11
α-helix	13-22	10
β-strand	25	1	12
β-strand	29-33	5	13
α-helix	39-42	4
β-strand	49-57	9	13
α-helix	60-76	17
β-strand	92	1	10
α-helix	95-105	11
α-helix	108-110	3
β-strand	113	1	12
α-helix	118-126	9
α-helix	131-139	9
α-helix	142-152	11
β-strand	155	1	14
α-helix	158-161	4
α-helix	165-166	2
β-strand	168-176	9	13
β-strand	179-183	5	13
β-strand	191-195	5	13
α-helix	201-215	15
β-strand	223-229	7	13

Chain E: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
β-strand	12-15	4	15
β-strand	22	1	16
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	15
β-strand	48-49	2	15
α-helix	50-51	2
β-strand	55	1	16
α-helix	57-59	3
β-strand	66-71	6	15
β-strand	74-75	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase isozyme L3	A, D	protein	227	Homo sapiens	P15374 (AlphaFold model)
Polyubiquitin-B	B, E	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Polyubiquitin-C	C, F	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6QML_1 Ubiquitin carboxyl-terminal hydrolase isozyme L3 (chains A, D)
QRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYE
VFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFL
EESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYEL
DGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA

Sequence of entity 2 (B, E), FASTA

>6QML_2 Polyubiquitin-B (chains B, E)
LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C, F), FASTA

>6QML_3 Polyubiquitin-C (chains C, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

K27-Linked Diubiquitin Inhibits UCHL3 via an Unusual Kinetic Trap. van Tilburg, G.B.A., Murachelli, A.G., Fish, A. et al. Cell Chem Biol (2021) 28:191-201.e8. DOI 10.1016/j.chembiol.2020.11.005 · PubMed

Other PDB entries of the same protein (UniProt P15374 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
7YV4 1.58 Å, Crystal structure of human UCHL3 in complex with Farrerol
1UCH 1.8 Å, Deubiquitinating enzyme uch-L3 (HUMAN) at 1.8 Å resolution
13DF 1.84 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(3-methoxyphenyl)benzamid…
6ISU 1.87 Å, Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting…
13CV 1.94 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(pyridin-2-yl)benzamide…
13CU 1.95 Å, Crystal structure of covalent inhibitor 2-chloro-N-(3-((pyridin-2-ylthio)methyl)phenyl)ac…
13CW 2.48 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(m-tolyl)benzamide bound…
35YH 2.6 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(3-hydroxyphenyl)benzamid…

Browse structure collections

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