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1XD3
Asym. Unit
Info
Asym.Unit (133 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (66 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF UCHL3-UBVME COMPLEX
Authors
:
S. Misaghi, P. J. Galardy, W. J. N. Meester, H. Ovaa, H. L. Ploegh, R. Gaudet
Date
:
03 Sep 04 (Deposition) - 23 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Enzyme-Ligand Complex, Active Site Crossover Loop, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Misaghi, P. J. Galardy, W. J. N. Meester, H. Ovaa, H. L. Ploegh, R. Gaudet
Structure Of The Ubiquitin Hydrolase Uch-L3 Complexed With A Suicide Substrate
J. Biol. Chem. V. 280 1512 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: METHYL 4-AMINOBUTANOATE (GVEa)
1b: METHYL 4-AMINOBUTANOATE (GVEb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GVE
2
Ligand/Ion
METHYL 4-AMINOBUTANOATE
2
MG
10
Ligand/Ion
MAGNESIUM ION
[
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]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:2246 , ASP C:163 , HOH C:2129 , HOH C:2193 , HOH C:2366
BINDING SITE FOR RESIDUE MG C 2001
02
AC2
SOFTWARE
HOH A:2123 , HOH A:2191 , HOH A:2227 , HOH C:2150 , HOH C:2194 , HOH C:2281
BINDING SITE FOR RESIDUE MG C 2002
03
AC3
SOFTWARE
HIS C:179 , HOH C:2184 , HOH C:2185 , HOH C:2191 , HOH C:2270 , HOH C:2374
BINDING SITE FOR RESIDUE MG C 2003
04
AC4
SOFTWARE
MG C:2005 , HOH C:2065 , HOH C:2072 , HOH C:2169 , HOH C:2190 , HOH C:2249 , HOH C:2397 , HOH C:2425
BINDING SITE FOR RESIDUE MG C 2004
05
AC5
SOFTWARE
GLN C:78 , ASP C:79 , MG C:2004 , HOH C:2169 , HOH C:2181 , HOH C:2190 , HOH C:2249
BINDING SITE FOR RESIDUE MG C 2005
06
AC6
SOFTWARE
LYS A:108 , ASP A:109 , HOH A:2346 , HOH B:1243
BINDING SITE FOR RESIDUE MG A 2006
07
AC7
SOFTWARE
GLU C:149 , HOH C:2069 , HOH C:2078 , HOH C:2433
BINDING SITE FOR RESIDUE MG C 2007
08
AC8
SOFTWARE
ASP C:79 , THR C:81 , TYR C:181
BINDING SITE FOR RESIDUE MG C 2008
09
AC9
SOFTWARE
HOH A:2264 , HOH A:2305 , HOH D:2344 , HOH D:2347 , HOH D:2354
BINDING SITE FOR RESIDUE MG A 2009
10
BC1
SOFTWARE
LYS A:21 , GLY A:24 , LEU A:25 , GLU A:114
BINDING SITE FOR RESIDUE MG A 2010
11
BC2
SOFTWARE
ILE A:58 , GLN A:89 , ASN A:93 , CYS A:95 , VAL A:166 , LEU A:168 , HIS A:169 , GLY B:75
BINDING SITE FOR RESIDUE GVE B 1176
12
BC3
SOFTWARE
GLN C:89 , ASN C:93 , CYS C:95 , VAL C:166 , LEU C:168 , HIS C:169 , HOH C:2432 , GLY D:75
BINDING SITE FOR RESIDUE GVE D 2276
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (B:1-75,D:1-75,B:1-75,D:1-75,-|-|B:...)
2: UBIQUITIN_1 (B:27-52,D:27-52,B:27-52,D:27-52,-|...)
3: UCH_1 (A:89-105,C:89-105)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_2
PS50053
Ubiquitin domain profile.
RS27A_HUMAN
1-76
2
B:1-75
D:1-75
RL40_HUMAN
1-76
2
B:1-75
D:1-75
UBB_HUMAN
1-76
77-152
153-228
2
-
-
B:1-75
D:1-75
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
2
-
-
-
-
-
-
-
-
B:1-75
D:1-75
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_HUMAN
27-52
2
B:27-52
D:27-52
RL40_HUMAN
27-52
2
B:27-52
D:27-52
UBB_HUMAN
27-52
103-128
179-204
2
-
-
B:27-52
D:27-52
UBC_HUMAN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
2
-
-
-
-
-
-
-
-
B:27-52
D:27-52
3
UCH_1
PS00140
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site.
UCHL3_HUMAN
89-105
2
A:89-105
C:89-105
[
close PROSITE info
]
Exons
(10, 20)
Info
All Exons
Exon 1.2 (B:1-75 | D:1-75)
Exon 2.2 (A:2-14 | C:4-14)
Exon 2.3 (A:15-18 | C:15-18)
Exon 2.4 (A:19-61 | C:19-61)
Exon 2.5a (A:62-114 | C:62-114)
Exon 2.6 (A:114-142 | C:114-142)
Exon 2.7 (A:143-158 | C:143-158)
Exon 2.9 (A:159-184 | C:159-184)
Exon 2.10 (A:184-203 | C:184-203)
Exon 2.11b (A:204-230 | C:204-230)
View:
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Label:
All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/-
03: Boundary -/2.2
04: Boundary 2.2/2.3
05: Boundary 2.3/2.4
06: Boundary 2.4/2.5a
07: Boundary 2.5a/2.6
08: Boundary 2.6/2.7
09: Boundary 2.7/2.9
10: Boundary 2.9/2.10
11: Boundary 2.10/2.11b
12: Boundary 2.11b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000339647
1
ENSE00001257182
chr12:
125399577-125399133
445
UBC_HUMAN
-
0
0
-
-
1.2
ENST00000339647
2
ENSE00001406973
chr12:
125398320-125396194
2127
UBC_HUMAN
1-686
686
2
B:1-75
D:1-75
75
75
2.2
ENST00000377595
2
ENSE00002160775
chr13:
76123927-76123998
72
UCHL3_HUMAN
1-14
14
2
A:2-14
C:4-14
13
11
2.3
ENST00000377595
3
ENSE00001785432
chr13:
76124112-76124123
12
UCHL3_HUMAN
15-18
4
2
A:15-18
C:15-18
4
4
2.4
ENST00000377595
4
ENSE00001596545
chr13:
76134889-76135017
129
UCHL3_HUMAN
19-61
43
2
A:19-61
C:19-61
43
43
2.5a
ENST00000377595
5a
ENSE00000684200
chr13:
76140831-76140987
157
UCHL3_HUMAN
62-114
53
2
A:62-114
C:62-114
53
53
2.6
ENST00000377595
6
ENSE00000684198
chr13:
76141363-76141448
86
UCHL3_HUMAN
114-142
29
2
A:114-142
C:114-142
29
29
2.7
ENST00000377595
7
ENSE00001349979
chr13:
76143596-76143643
48
UCHL3_HUMAN
143-158
16
2
A:143-158
C:143-158
16
16
2.9
ENST00000377595
9
ENSE00000684194
chr13:
76169051-76169126
76
UCHL3_HUMAN
159-184
26
2
A:159-184
C:159-184
26
26
2.10
ENST00000377595
10
ENSE00000684192
chr13:
76178905-76178963
59
UCHL3_HUMAN
184-203
20
2
A:184-203
C:184-203
20
20
2.11b
ENST00000377595
11b
ENSE00001853190
chr13:
76179865-76180069
205
UCHL3_HUMAN
204-230
27
2
A:204-230
C:204-230
27
27
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1xd3b_ (B:)
1b: SCOP_d1xd3d_ (D:)
2a: SCOP_d1xd3a_ (A:)
2b: SCOP_d1xd3c_ (C:)
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Folds
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(
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Families
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
Ubiquitin-related
(337)
Protein domain
:
Ubiquitin
(162)
Human (Homo sapiens) [TaxId: 9606]
(121)
1a
d1xd3b_
B:
1b
d1xd3d_
D:
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Ubiquitin carboxyl-terminal hydrolase UCH-L
(10)
Protein domain
:
Ubiquitin carboxyl-terminal hydrolase UCH-l3
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d1xd3a_
A:
2b
d1xd3c_
C:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1xd3C00 (C:4-230)
1b: CATH_1xd3A00 (A:2-230)
2a: CATH_1xd3B00 (B:1-75)
2b: CATH_1xd3D00 (D:1-75)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Ubiquitin C-terminal Hydrolase UCH-l3
(8)
Homologous Superfamily
:
Ubiquitin C-terminal Hydrolase Uch-l3
(8)
Human (Homo sapiens)
(7)
1a
1xd3C00
C:4-230
1b
1xd3A00
A:2-230
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
(286)
Human (Homo sapiens)
(177)
2a
1xd3B00
B:1-75
2b
1xd3D00
D:1-75
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain C
Chain D
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