1XD3: UCHL3-UbVME complex

Name: PDB 1XD3: Crystal structure of UCHL3-UbVME complex
Published: 2004-11-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Crystal structure of UCHL3-UbVME complex. Determined by X-ray diffraction at 1.45 Å resolution. Released 23 Nov 2004.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,182
Mol. weight: 69.94 kDa
Ligands: MG, GVE
Released: 23 Nov 2004

Explore 1XD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1XD3 contains 28 α-helices and 38 β-strands across 4 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
α-helix	7-9	3
β-strand	10	1	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	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: 3 helices, 8 β-strands

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

Chain C: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
α-helix	7-9	3
β-strand	10	1	8
α-helix	13-22	10
β-strand	25	1	9
β-strand	29-33	5	10
α-helix	39-42	4
β-strand	49-57	9	10
α-helix	60-76	17
β-strand	92	1	7
α-helix	95-105	11
α-helix	108-110	3
β-strand	113	1	9
α-helix	118-126	9
α-helix	131-139	9
α-helix	142-152	11
α-helix	158-161	4
β-strand	168-176	9	10
β-strand	179-183	5	10
β-strand	191-195	5	10
α-helix	201-214	14
β-strand	223-229	7	10

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
β-strand	12-16	5	11
β-strand	22	1	12
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	11
β-strand	48-49	2	11
α-helix	50-51	2
β-strand	55	1	12
α-helix	57-59	3
β-strand	66-71	6	11
β-strand	74	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin Carboxyl-terminal esterase L3	A, C	protein	230	Homo sapiens	P15374 (AlphaFold model)
UBC protein	B, D	protein	75	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1XD3_1 Ubiquitin Carboxyl-terminal esterase L3 (chains A, C)
MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITE
KYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLK
KFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHL
YELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA

Sequence of entity 2 (B, D), FASTA

>1XD3_2 UBC protein (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	10
GVE	Methyl 4-aminobutanoate	C5 H11 N O2	2

Primary citation

Structure of the Ubiquitin Hydrolase UCH-L3 Complexed with a Suicide Substrate. Misaghi, S., Galardy, P.J., Meester, W.J.N. et al. J Biol Chem (2005) 280:1512-1520. DOI 10.1074/jbc.M410770200 · PubMed

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

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…
6QML 2.1 Å, UCHL3 in complex with synthetic, K27-linked diubiquitin
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…

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