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3I3T
Biol. Unit 4
Info
Asym.Unit (259 KB)
Biol.Unit 1 (66 KB)
Biol.Unit 2 (67 KB)
Biol.Unit 3 (68 KB)
Biol.Unit 4 (67 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF COVALENT UBIQUITIN-USP21 COMPLEX
Authors
:
D. Neculai, G. V. Avvakumov, J. R. Walker, S. Xue, C. Butler-Cole, J. Wei C. Bountra, A. M. Edwards, C. H. Arrowsmith, A. Bochkarev, S. Dhe-Paga Structural Genomics Consortium (Sgc)
Date
:
30 Jun 09 (Deposition) - 21 Jul 09 (Release) - 27 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.59
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Ubiquitin-Specific Protease Activity, Hydrolase, Ubiquitin Biology, Structural Genomics Consortium, Sgc, Activator, Chromatin Regulator, Nucleus, Protease, Thiol Protease, Transcription, Transcription Regulation, Ubl Conjugation Pathway, Isopeptide Bond, Phosphoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Ernst, G. Avvakumov, J. Tong, Y. Fan, Y. Zhao, P. Alberts, A. Persaud J. R. Walker, A. M. Neculai, D. Neculai, A. Vorobyov, P. Garg, L. Beatty P. K. Chan, Y. C. Juang, M. C. Landry, C. Yeh, E. Zeqiraj, K. Karamboulas A. Allali-Hassani, M. Vedadi, M. Tyers, J. Moffat, F. Sicheri, L. Pelletier, D. Durocher, B. Raught, D. Rotin, J. Yang, M. F. Moran, S. Dhe-Paganon, S. S. Sidhu
A Strategy For Modulation Of Enzymes In The Ubiquitin System.
Science V. 339 590 2013
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: ETHANAMINE (NEHa)
1b: ETHANAMINE (NEHb)
1c: ETHANAMINE (NEHc)
1d: ETHANAMINE (NEHd)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NEH
1
Ligand/Ion
ETHANAMINE
2
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(2, 2)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
CYS G:384 , CYS G:387 , CYS G:437 , CYS G:440
BINDING SITE FOR RESIDUE ZN G 700
2
AC8
SOFTWARE
ASN G:219 , CYS G:221 , GLN G:299 , GLY G:517 , GLY H:75
BINDING SITE FOR RESIDUE NEH H 76
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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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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(5, 11)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (H:1-75)
2: UBIQUITIN_1 (H:27-52)
3: USP_3 (G:212-558)
4: USP_1 (G:213-228)
5: USP_2 (G:502-519)
;
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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
-
-
-
H:1-75
RL40_HUMAN
1-76
1
-
-
-
H:1-75
UBB_HUMAN
1-76
77-152
153-228
1
-
-
-
-
-
H:1-75
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
1
-
-
-
-
-
-
-
-
-
-
-
H:1-75
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_HUMAN
27-52
1
-
-
-
H:27-52
RL40_HUMAN
27-52
1
-
-
-
H:27-52
UBB_HUMAN
27-52
103-128
179-204
1
-
-
-
-
-
H:27-52
UBC_HUMAN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
1
-
-
-
-
-
-
-
-
-
-
-
H:27-52
3
USP_3
PS50235
Ubiquitin specific protease (USP) domain profile.
UBP21_HUMAN
212-558
1
-
-
-
G:212-558
4
USP_1
PS00972
Ubiquitin specific protease (USP) domain signature 1.
UBP21_HUMAN
213-228
1
-
-
-
G:213-228
5
USP_2
PS00973
Ubiquitin specific protease (USP) domain signature 2.
UBP21_HUMAN
502-519
1
-
-
-
G:502-519
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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, 8)
Info
All SCOP Domains
1a: SCOP_d3i3tb_ (B:)
1b: SCOP_d3i3td_ (D:)
1c: SCOP_d3i3tf_ (F:)
1d: SCOP_d3i3th_ (H:)
2a: SCOP_d3i3ta_ (A:)
2b: SCOP_d3i3tc_ (C:)
2c: SCOP_d3i3te_ (E:)
2d: SCOP_d3i3tg_ (G:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d3i3tb_
B:
1b
d3i3td_
D:
1c
d3i3tf_
F:
1d
d3i3th_
H:
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
automated matches
(52)
Protein domain
:
automated matches
(52)
Human (Homo sapiens) [TaxId: 9606]
(30)
2a
d3i3ta_
A:
2b
d3i3tc_
C:
2c
d3i3te_
E:
2d
d3i3tg_
G:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3i3tB00 (B:1-75)
1b: CATH_3i3tD00 (D:1-75)
1c: CATH_3i3tF00 (F:1-75)
1d: CATH_3i3tH00 (H:1-75)
View:
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(
)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
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)
1a
3i3tB00
B:1-75
1b
3i3tD00
D:1-75
1c
3i3tF00
F:1-75
1d
3i3tH00
H: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
Protein & NOT PROSITE
Chain G
Chain H
Asymmetric Unit 1
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Miscellaneous
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Example Commands
Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (259 KB)
Header - Asym.Unit
Biol.Unit 1 (66 KB)
Header - Biol.Unit 1
Biol.Unit 2 (67 KB)
Header - Biol.Unit 2
Biol.Unit 3 (68 KB)
Header - Biol.Unit 3
Biol.Unit 4 (67 KB)
Header - Biol.Unit 4
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