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2Y6E
Asym. Unit
Info
Asym.Unit (706 KB)
Biol.Unit 1 (695 KB)
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(1)
Title
:
STRUCTURE OF THE D1D2 DOMAIN OF USP4, THE CONSERVED CATALYTIC DOMAIN
Authors
:
M. P. A. Luna-Vargas, A. C. Faesen, W. J. Van Dijk, M. Rape, A. Fish, T. K.
Date
:
20 Jan 11 (Deposition) - 06 Apr 11 (Release) - 03 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Clerici, M. P. A. Luna-Vargas, A. C. Faesen, T. K. Sixma
The Dusp-Ubl Domain Of Usp4 Enhances Its Catalytic Efficiency By Promoting Ubiquitin Exchange.
Nat. Commun. V. 5 5399 2014
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEa)
1b: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEb)
1c: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEc)
1d: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEd)
1e: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEe)
1f: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
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No.
Name
Count
Type
Full Name
1
CME
6
Mod. Amino Acid
S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2
SO4
2
Ligand/Ion
SULFATE ION
3
ZN
6
Ligand/Ion
ZINC ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:461 , CYS A:464 , CYS A:799 , CYS A:802
BINDING SITE FOR RESIDUE ZN A1000
2
AC2
SOFTWARE
GLN A:391 , MET A:877 , GLY A:878 , HOH A:2248 , HOH A:2249 , ARG B:373 , LYS C:348 , ARG C:381
BINDING SITE FOR RESIDUE SO4 A1926
3
AC3
SOFTWARE
CYS B:461 , CYS B:464 , CYS B:799 , CYS B:802
BINDING SITE FOR RESIDUE ZN B1000
4
AC4
SOFTWARE
CYS C:461 , CYS C:464 , CYS C:799 , CYS C:802
BINDING SITE FOR RESIDUE ZN C1000
5
AC5
SOFTWARE
TYR C:476 , THR C:478
BINDING SITE FOR RESIDUE SO4 C1925
6
AC6
SOFTWARE
CYS D:461 , CYS D:464 , CYS D:799 , CYS D:802
BINDING SITE FOR RESIDUE ZN D1000
7
AC7
SOFTWARE
CYS E:461 , CYS E:464
BINDING SITE FOR RESIDUE ZN E1000
8
AC8
SOFTWARE
CYS F:461 , CYS F:464
BINDING SITE FOR RESIDUE ZN F1000
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(3, 18)
Info
All PROSITE Patterns/Profiles
1: USP_3 (A:302-923,B:302-923,C:302-923,D:30...)
2: USP_1 (A:303-318,B:303-318,C:303-318,D:30...)
3: USP_2 (A:865-882,B:865-882,C:865-882,D:86...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
USP_3
PS50235
Ubiquitin specific protease (USP) domain profile.
UBP4_HUMAN
302-923
6
A:302-923
B:302-923
C:302-923
D:302-923
E:302-923
F:302-923
2
USP_1
PS00972
Ubiquitin specific protease (USP) domain signature 1.
UBP4_HUMAN
303-318
6
A:303-318
B:303-318
C:303-318
D:303-318
E:303-318
F:303-318
3
USP_2
PS00973
Ubiquitin specific protease (USP) domain signature 2.
UBP4_HUMAN
865-882
6
A:865-882
B:865-882
C:865-882
D:865-882
E:865-882
F:865-882
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_UCH_2y6eF01 (F:299-920)
1b: PFAM_UCH_2y6eF02 (F:299-920)
1c: PFAM_UCH_2y6eF03 (F:299-920)
1d: PFAM_UCH_2y6eF04 (F:299-920)
1e: PFAM_UCH_2y6eF05 (F:299-920)
1f: PFAM_UCH_2y6eF06 (F:299-920)
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Clan
:
Peptidase_CA
(169)
Family
:
UCH
(11)
Homo sapiens (Human)
(6)
1a
UCH-2y6eF01
F:299-920
1b
UCH-2y6eF02
F:299-920
1c
UCH-2y6eF03
F:299-920
1d
UCH-2y6eF04
F:299-920
1e
UCH-2y6eF05
F:299-920
1f
UCH-2y6eF06
F:299-920
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Asymmetric Unit 1
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