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1XD3
Biol. Unit 2
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
(1, 1)
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
1
Ligand/Ion
METHYL 4-AMINOBUTANOATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC7 (SOFTWARE)
7: AC8 (SOFTWARE)
8: AC9 (SOFTWARE)
9: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:2246 , ASP C:163 , HOH C:2129 , HOH C:2193 , HOH C:2366
BINDING SITE FOR RESIDUE MG C 2001
2
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
3
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
4
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
5
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
6
AC7
SOFTWARE
GLU C:149 , HOH C:2069 , HOH C:2078 , HOH C:2433
BINDING SITE FOR RESIDUE MG C 2007
7
AC8
SOFTWARE
ASP C:79 , THR C:81 , TYR C:181
BINDING SITE FOR RESIDUE MG C 2008
8
AC9
SOFTWARE
HOH A:2264 , HOH A:2305 , HOH D:2344 , HOH D:2347 , HOH D:2354
BINDING SITE FOR RESIDUE MG A 2009
9
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 only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 9)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (D:1-75)
2: UBIQUITIN_1 (D:27-52)
3: UCH_1 (C:89-105)
;
View:
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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
1
-
D:1-75
RL40_HUMAN
1-76
1
-
D:1-75
UBB_HUMAN
1-76
77-152
153-228
1
-
-
-
D:1-75
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
1
-
-
-
-
-
-
-
-
-
D:1-75
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_HUMAN
27-52
1
-
D:27-52
RL40_HUMAN
27-52
1
-
D:27-52
UBB_HUMAN
27-52
103-128
179-204
1
-
-
-
D:27-52
UBC_HUMAN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
1
-
-
-
-
-
-
-
-
-
D:27-52
3
UCH_1
PS00140
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site.
UCHL3_HUMAN
89-105
1
-
C:89-105
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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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Classes
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(
)
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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:
[
close SCOP info
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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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Protein & NOT Site
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Chain C
Chain D
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (133 KB)
Header - Asym.Unit
Biol.Unit 1 (65 KB)
Header - Biol.Unit 1
Biol.Unit 2 (66 KB)
Header - Biol.Unit 2
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