Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6QML

UCHL3 in complex with synthetic, K27-linked diubiquitin

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006508	biological_process	proteolysis
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0008233	molecular_function	peptidase activity
A	0008234	molecular_function	cysteine-type peptidase activity
A	0016567	biological_process	protein ubiquitination
A	0016579	biological_process	protein deubiquitination
A	0016787	molecular_function	hydrolase activity
A	0019784	molecular_function	deNEDDylase activity
A	0030163	biological_process	protein catabolic process
A	0043130	molecular_function	ubiquitin binding
A	0043687	biological_process	post-translational protein modification
A	0101005	molecular_function	deubiquitinase activity
D	0004843	molecular_function	cysteine-type deubiquitinase activity
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006508	biological_process	proteolysis
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0008233	molecular_function	peptidase activity
D	0008234	molecular_function	cysteine-type peptidase activity
D	0016567	biological_process	protein ubiquitination
D	0016579	biological_process	protein deubiquitination
D	0016787	molecular_function	hydrolase activity
D	0019784	molecular_function	deNEDDylase activity
D	0030163	biological_process	protein catabolic process
D	0043130	molecular_function	ubiquitin binding
D	0043687	biological_process	post-translational protein modification
D	0101005	molecular_function	deubiquitinase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue K A 301

Chain	Residue
A	ASN106
A	ASN107
A	HIS175
A	HOH409

site_id	AC2
Number of Residues	6
Details	binding site for residue EDO A 304

Chain	Residue
D	ALA143
A	ASP142
A	EDO307
D	LYS121
D	TYR141
D	ASP142

site_id	AC3
Number of Residues	5
Details	binding site for residue EDO A 305

Chain	Residue
A	ASP33
A	MET44
A	VAL45
A	HOH406
A	HOH458

site_id	AC4
Number of Residues	4
Details	binding site for residue EDO A 306

Chain	Residue
A	GLN30
A	SER228
A	ALA229
A	ALA230

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO A 307

Chain	Residue
A	ASP142
A	ALA143
A	EDO304
D	K303

site_id	AC6
Number of Residues	1
Details	binding site for residue BR B 101

Chain	Residue
B	GLU16

site_id	AC7
Number of Residues	4
Details	binding site for residue EDO B 102

Chain	Residue
A	MET213
A	PRO217
B	THR9
B	HOH210

site_id	AC8
Number of Residues	5
Details	binding site for residue EDO B 103

Chain	Residue
A	GLU40
B	ILE44
B	ALA46
B	GLY47
B	HIS68

site_id	AC9
Number of Residues	1
Details	binding site for residue BR C 101

Chain	Residue
C	GLY75

site_id	AD1
Number of Residues	4
Details	binding site for residue EDO C 102

Chain	Residue
C	LEU15
C	GLU16
C	LYS29
C	LYS33

site_id	AD2
Number of Residues	4
Details	binding site for residue EDO C 103

Chain	Residue
C	LYS6
C	HIS68
C	HOH214
D	GLY116

site_id	AD3
Number of Residues	4
Details	binding site for residue EDO C 104

Chain	Residue
C	THR7
C	LEU8
C	LEU69
C	LEU71

site_id	AD4
Number of Residues	4
Details	binding site for residue K D 301

Chain	Residue
D	ASN106
D	ASN107
D	HIS175
D	HOH414

site_id	AD5
Number of Residues	6
Details	binding site for residue K D 302

Chain	Residue
A	ASN140
A	ASP142
A	HOH478
D	ASN140
D	ASP142
D	HOH449

site_id	AD6
Number of Residues	4
Details	binding site for residue K D 303

Chain	Residue
A	ALA143
A	EDO307
A	HOH486
D	ASP142

site_id	AD7
Number of Residues	3
Details	binding site for residue EDO D 304

Chain	Residue
D	VAL84
D	VAL127
D	ARG134

site_id	AD8
Number of Residues	2
Details	binding site for residue EDO D 305

Chain	Residue
D	PRO190
D	HOH431

site_id	AD9
Number of Residues	8
Details	binding site for residue EDO D 306

Chain	Residue
D	ARG47
D	PRO48
D	VAL49
D	ASP198
D	GLU199
D	LEU201
D	LEU202
D	HOH406

site_id	AE1
Number of Residues	4
Details	binding site for residue EDO D 307

Chain	Residue
A	PHE65
A	GLU69
A	ILE191
D	GLN76

site_id	AE2
Number of Residues	1
Details	binding site for residue BR F 101

Chain	Residue
F	GLU16

site_id	AE3
Number of Residues	7
Details	binding site for residue EDO F 102

Chain	Residue
F	ILE44
F	PHE45
F	ALA46
F	GLY47
F	THR66
F	HIS68
F	HOH205

site_id	AE4
Number of Residues	6
Details	binding site for residue EDO F 103

Chain	Residue
A	GLY116
F	LYS6
F	THR66
F	HIS68
F	HOH209
F	HOH213

site_id	AE5
Number of Residues	10
Details	binding site for Di-peptide NLE E 1 and GLN E 2

Chain	Residue
E	LYS63
E	GLU64
A	GLU164
B	PRO37
B	ASP39
E	ILE3
E	THR14
E	LEU15
E	GLU16
E	VAL17

site_id	AE6
Number of Residues	33
Details	binding site for Di-peptide LYS E 27 and GLY F 76

Chain	Residue
D	GLN89
D	ASN93
D	CYS95
D	VAL166
D	LEU168
D	HIS169
E	ILE23
E	GLU24
E	ASN25
E	VAL26
E	ALA28
E	LYS29
E	ILE30
E	GLN31
E	GLN41
E	ARG42
E	LEU43
E	LEU50
E	ASP52
E	GLY75
F	ILE23
F	GLU24
F	ASN25
F	VAL26
F	ALA28
F	LYS29
F	ILE30
F	GLN31
F	GLN41
F	ASP52
F	GLY75
F	HOH201
F	HOH212

site_id	AE7
Number of Residues	24
Details	binding site for Di-peptide GLY E 76 and CYS D 95

Chain	Residue
A	GLN78
A	ASP79
A	ASN192
A	HIS193
A	GLY194
D	LYS72
D	ILE73
D	LYS74
D	SER75
D	GLY77
D	GLN89
D	ASN93
D	ALA94
D	GLY96
D	THR97
D	ILE98
D	GLY99
D	VAL166
D	LEU168
D	HIS169
D	PHE170
D	EDO307
D	HOH442
E	GLY75

Functional Information from PROSITE/UniProt

site_id	PS00140
Number of Residues	17
Details	UCH_1 Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. QtisNACGtigLIHAIA

Chain	Residue	Details
A	GLN89-ALA105

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
B	LYS27-ASP52
C	LYS27-ASP52

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	448
Details	Domain: {"description":"UCH catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	20
Details	Region: {"description":"Interaction with ubiquitin","evidences":[{"source":"PubMed","id":"15531586","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	14
Details	Region: {"description":"Interaction with ubiquitin. Crossover loop which restricts access of large ubiquitin adducts to the active site","evidences":[{"source":"PubMed","id":"15531586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19047059","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19154770","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20380862","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9790970","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Active site: {"description":"Proton donor","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Site: {"description":"Transition state stabilizer","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Site: {"description":"Important for enzyme activity","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	150
Details	Domain: {"description":"Ubiquitin-like 9","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 597

Chain	Residue	Details
A	GLN89	electrostatic stabiliser
A	CYS95	covalent catalysis, proton shuttle (general acid/base)
A	HIS169	proton shuttle (general acid/base)
A	ASP184	electrostatic stabiliser

site_id	MCSA2
Number of Residues	4
Details	M-CSA 597

Chain	Residue	Details
D	GLN89	electrostatic stabiliser
D	CYS95	covalent catalysis, proton shuttle (general acid/base)
D	HIS169	proton shuttle (general acid/base)
D	ASP184	electrostatic stabiliser

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)