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3SDK
Asym. Unit
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Asym.Unit (994 KB)
Biol.Unit 1 (985 KB)
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(1)
Title
:
STRUCTURE OF YEAST 20S OPEN-GATE PROTEASOME WITH COMPOUND 34
Authors
:
M. D. Sintchak
Date
:
09 Jun 11 (Deposition) - 13 Jun 12 (Release) - 03 Apr 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2 (1x)
Keywords
:
20S Proteasome, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Blackburn, C. Barrett, J. L. Blank, F. J. Bruzzese, N. Bump, L. R. Dick, P. Fleming, K. Garcia, P. Hales, Z. Hu, M. Jones, J. X. Liu, D. S. Sappal, M. D. Sintchak, C. Tsu, K. M. Gigstad
Optimization Of A Series Of Dipeptides With A P3 Threonine Residue As Non-Covalent Inhibitors Of The Chymotrypsin-Like Activity Of The Human 20S Proteasome.
Bioorg. Med. Chem. Lett. V. 20 6581 2010
[
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
1b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
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)
3a: N-[(2S)-3-(3-TERT-BUTYL-1,2,4-OXAD... (P3Na)
3b: N-[(2S)-3-(3-TERT-BUTYL-1,2,4-OXAD... (P3Nb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2
MG
10
Ligand/Ion
MAGNESIUM ION
3
P3N
2
Ligand/Ion
N-[(2S)-3-(3-TERT-BUTYL-1,2,4-OXADIAZOL-5-YL)-1-({(2S)-1-[(4-METHYLBENZYL)AMINO]-1-OXO-4-PHENYLBUTAN-2-YL}AMINO)-1-OXOPROPAN-2-YL]-5-METHYL-1,2-OXAZOLE-3-CARBOXAMIDE
[
close Hetero Component info
]
Sites
(14, 14)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET F:150 , ALA F:164 , THR F:165 , ARG F:169 , LYS F:173
BINDING SITE FOR RESIDUE MG F 301
02
AC2
SOFTWARE
SER F:13 , ASN F:127 , ALA G:127 , TYR G:128
BINDING SITE FOR RESIDUE MG F 302
03
AC3
SOFTWARE
THR G:13 , TYR G:123 , ARG G:126 , ALA G:127 , MET G:129
BINDING SITE FOR RESIDUE MG G 301
04
AC4
SOFTWARE
GLY H:162 , ILE H:163 , ASP H:166 , SER H:169 , ASP Z:194
BINDING SITE FOR RESIDUE MG H 301
05
AC5
SOFTWARE
GLY I:128 , SER I:131
BINDING SITE FOR RESIDUE MG I 201
06
AC6
SOFTWARE
ALA I:163 , ASP I:166 , SER I:169
BINDING SITE FOR RESIDUE MG I 202
07
AC7
SOFTWARE
ALA K:163 , ASP K:166 , SER K:169 , ASP W:194
BINDING SITE FOR RESIDUE MG K 301
08
AC8
SOFTWARE
THR K:1 , ALA K:20 , THR K:21 , ALA K:27 , VAL K:31 , LYS K:33 , GLY K:47 , ALA K:49 , MES K:303 , ASP L:114 , PRO L:115
BINDING SITE FOR RESIDUE P3N K 302
09
AC9
SOFTWARE
THR K:1 , GLY K:47 , GLY K:128 , SER K:129 , P3N K:302
BINDING SITE FOR RESIDUE MES K 303
10
BC1
SOFTWARE
GLU D:105 , SER L:75 , SER L:78
BINDING SITE FOR RESIDUE MG L 201
11
BC2
SOFTWARE
THR L:163 , HIS L:166 , VAL L:169
BINDING SITE FOR RESIDUE MG L 202
12
BC3
SOFTWARE
ILE N:163 , ASP N:166 , SER N:169
BINDING SITE FOR RESIDUE MG N 201
13
BC4
SOFTWARE
THR Y:1 , ALA Y:20 , THR Y:21 , ALA Y:27 , VAL Y:31 , LYS Y:33 , GLY Y:47 , ALA Y:49 , SER Y:96 , ASP Z:114 , VAL Z:116
BINDING SITE FOR RESIDUE P3N Y 301
14
BC5
SOFTWARE
THR Y:1 , GLY Y:47 , GLY Y:128 , SER Y:129
BINDING SITE FOR RESIDUE MES Y 302
[
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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
(4, 44)
Info
All PROSITE Patterns/Profiles
1: PROTEASOME_BETA_2 (J:-1-178,X:-1-178,I:-1-178,W:-1-17...)
2: PROTEASOME_ALPHA_1 (C:8-30,Q:8-30,A:8-30,O:8-30,E:8-30...)
3: PROTEASOME_BETA_1 (J:4-51,X:4-51,I:4-51,W:4-51,2:4-51...)
4: PROTEASOME_ALPHA_2 (C:23-233,Q:23-233,A:23-233,O:23-23...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEASOME_BETA_2
PS51476
Proteasome beta-type subunit profile.
PSB4_YEAST
1-184
2
J:-1-178
X:-1-178
PSB3_YEAST
9-190
2
I:-1-178
W:-1-178
PSB6_YEAST
28-226
2
L:-1-178
Z:-1-178
PSB7_YEAST
41-233
2
1:-1-178
M:-1-178
2
PROTEASOME_ALPHA_1
PS00388
Proteasome alpha-type subunits signature.
PSA4_YEAST
4-26
2
C:8-30
Q:8-30
PSA2_YEAST
5-27
2
A:8-30
O:8-30
PSA6_YEAST
6-28
2
E:8-30
S:8-30
PSA1_YEAST
12-34
2
G:8-30
U:8-30
3
PROTEASOME_BETA_1
PS00854
Proteasome beta-type subunits signature.
PSB4_YEAST
5-52
2
J:4-51
X:4-51
PSB3_YEAST
13-59
2
I:4-51
W:4-51
PSB1_YEAST
23-70
2
2:4-51
N:4-51
PSB6_YEAST
32-79
2
L:4-51
Z:4-51
PSB2_YEAST
33-80
2
H:4-51
V:4-51
PSB7_YEAST
45-92
2
1:4-51
M:4-51
PSB5_YEAST
79-126
2
K:4-51
Y:4-51
4
PROTEASOME_ALPHA_2
PS51475
Proteasome alpha-type subunit profile.
PSA4_YEAST
19-233
2
C:23-233
Q:23-233
PSA2_YEAST
20-247
2
A:23-233
O:23-233
PSA6_YEAST
21-234
2
E:23-233
S:23-233
PSA3_YEAST
21-239
2
B:23-233
P:23-233
PSA5_YEAST
23-240
2
D:23-233
R:23-233
PSA7_YEAST
23-240
2
F:23-233
T:23-233
PSA1_YEAST
27-245
2
G:23-233
U:23-233
[
close PROSITE info
]
Exons
(15, 30)
Info
All Exons
Exon 1.1 (L:-9-194 (gaps) | Z:-9-194 (gaps))
Exon 2.1 (J:-1-193 (gaps) | X:-1-193 (gaps))
Exon 3.1 (I:-8-194 (gaps) | W:-8-194 (gaps))
Exon 4.1 (1:-8-211 (gaps) | M:-8-211 (gaps))
Exon 5.1 (G:6-240 (gaps) | U:6-240 (gaps))
Exon 6.1 (B:13-239 (gaps) | P:13-239 (gaps))
Exon 7.1 (D:9-244 (gaps) | R:9-244 (gaps))
Exon 8.1 (2:1-3 | N:1-3)
Exon 8.2 (2:3-187J (gaps) | N:3-187J (gaps))
Exon 9.1 (A:4-236 (gaps) | O:4-236 (gaps))
Exon 10.1 (E:4-233 (gaps) | S:4-233 (gaps))
Exon 11.1 (C:7-243 (gaps) | Q:7-243 (gaps))
Exon 12.1 (H:1-223 (gaps) | V:1-223 (gaps))
Exon 13.1 (F:13-241 (gaps) | T:13-241 (gaps))
Exon 14.1 (K:1-211 (gaps) | Y:1-211 (gaps))
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/-
03: Boundary -/2.1
04: Boundary 2.1/-
05: Boundary -/3.1
06: Boundary 3.1/-
07: Boundary -/4.1
08: Boundary 4.1/-
09: Boundary -/5.1
10: Boundary 5.1/-
11: Boundary -/6.1
12: Boundary 6.1/-
13: Boundary -/7.1
14: Boundary 7.1/-
15: Boundary -/8.1
16: Boundary 8.1/8.2
17: Boundary 8.2/-
18: Boundary -/9.1
19: Boundary 9.1/-
20: Boundary -/10.1
21: Boundary 10.1/-
22: Boundary -/11.1
23: Boundary 11.1/-
24: Boundary -/12.1
25: Boundary 12.1/-
26: Boundary -/13.1
27: Boundary 13.1/-
28: Boundary -/14.1
29: Boundary 14.1/-
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
YBL041W
1
YBL041W.1
II:141250-141975
726
PSB6_YEAST
1-241
241
2
L:-9-194 (gaps)
Z:-9-194 (gaps)
223
223
2.1
YER012W
1
YER012W.1
V:177834-178430
597
PSB4_YEAST
1-198
198
2
J:-1-193 (gaps)
X:-1-193 (gaps)
199
199
3.1
YER094C
1
YER094C.1
V:349342-348725
618
PSB3_YEAST
1-205
205
2
I:-8-194 (gaps)
W:-8-194 (gaps)
206
206
4.1
YFR050C
1
YFR050C.1
VI:249853-249053
801
PSB7_YEAST
1-266
266
2
1:-8-211 (gaps)
M:-8-211 (gaps)
236
236
5.1
YGL011C
1
YGL011C.1
VII:475252-474494
759
PSA1_YEAST
1-252
252
2
G:6-240 (gaps)
U:6-240 (gaps)
248
244
6.1
YGR135W
1
YGR135W.1
VII:761397-762173
777
PSA3_YEAST
1-258
258
2
B:13-239 (gaps)
P:13-239 (gaps)
236
236
7.1
YGR253C
1
YGR253C.1
VII:999145-998363
783
PSA5_YEAST
1-260
260
2
D:9-244 (gaps)
R:9-244 (gaps)
248
245
8.1
YJL001W
1
YJL001W.1
X:435156-435220
65
PSB1_YEAST
1-22
22
2
2:1-3
N:1-3
3
3
8.2
YJL001W
2
YJL001W.2
X:435337-435919
583
PSB1_YEAST
22-215
194
2
2:3-187J (gaps)
N:3-187J (gaps)
197
197
9.1
YML092C
1
YML092C.1
XIII:86739-85987
753
PSA2_YEAST
1-250
250
2
A:4-236 (gaps)
O:4-236 (gaps)
251
251
10.1
YMR314W
1
YMR314W.1
XIII:901708-902412
705
PSA6_YEAST
1-234
234
2
E:4-233 (gaps)
S:4-233 (gaps)
240
236
11.1
YOL038W
1
YOL038W.1
XV:255336-256100
765
PSA4_YEAST
1-254
254
2
C:7-243 (gaps)
Q:7-243 (gaps)
244
244
12.1
YOR157C
1
YOR157C.1
XV:631752-630967
786
PSB2_YEAST
1-261
261
2
H:1-223 (gaps)
V:1-223 (gaps)
224
224
13.1
YOR362C
1
YOR362C.1
XV:1018744-1017878
867
PSA7_YEAST
1-288
288
2
F:13-241 (gaps)
T:13-241 (gaps)
240
237
14.1
YPR103W
1
YPR103W.1
XVI:732347-733210
864
PSB5_YEAST
1-287
287
2
K:1-211 (gaps)
Y:1-211 (gaps)
213
213
[
close EXON info
]
SCOP Domains
(3, 28)
Info
All SCOP Domains
1a: SCOP_d3sdkb_ (B:)
1b: SCOP_d3sdkd_ (D:)
1c: SCOP_d3sdkp_ (P:)
1d: SCOP_d3sdkr_ (R:)
2a: SCOP_d3sdkf_ (F:)
2b: SCOP_d3sdkt_ (T:)
3a: SCOP_d3sdk1_ (1:)
3b: SCOP_d3sdk2_ (2:)
3c: SCOP_d3sdka_ (A:)
3d: SCOP_d3sdkc_ (C:)
3e: SCOP_d3sdke_ (E:)
3f: SCOP_d3sdkg_ (G:)
3g: SCOP_d3sdkh_ (H:)
3h: SCOP_d3sdki_ (I:)
3i: SCOP_d3sdkj_ (J:)
3j: SCOP_d3sdkk_ (K:)
3k: SCOP_d3sdkl_ (L:)
3l: SCOP_d3sdkm_ (M:)
3m: SCOP_d3sdkn_ (N:)
3n: SCOP_d3sdko_ (O:)
3o: SCOP_d3sdkq_ (Q:)
3p: SCOP_d3sdks_ (S:)
3q: SCOP_d3sdku_ (U:)
3r: SCOP_d3sdkv_ (V:)
3s: SCOP_d3sdkw_ (W:)
3t: SCOP_d3sdkx_ (X:)
3u: SCOP_d3sdky_ (Y:)
3v: SCOP_d3sdkz_ (Z:)
View:
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Classes
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)
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Folds
(
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(
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(
)
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ntn hydrolase-like
(356)
Superfamily
:
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
(352)
Family
:
Proteasome subunits
(222)
Protein domain
:
automated matches
(78)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292]
(19)
1a
d3sdkb_
B:
1b
d3sdkd_
D:
1c
d3sdkp_
P:
1d
d3sdkr_
R:
Protein domain
:
Proteasome alpha subunit (non-catalytic)
(66)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(54)
2a
d3sdkf_
F:
2b
d3sdkt_
T:
Protein domain
:
Proteasome beta subunit (catalytic)
(61)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(51)
3a
d3sdk1_
1:
3b
d3sdk2_
2:
3c
d3sdka_
A:
3d
d3sdkc_
C:
3e
d3sdke_
E:
3f
d3sdkg_
G:
3g
d3sdkh_
H:
3h
d3sdki_
I:
3i
d3sdkj_
J:
3j
d3sdkk_
K:
3k
d3sdkl_
L:
3l
d3sdkm_
M:
3m
d3sdkn_
N:
3n
d3sdko_
O:
3o
d3sdkq_
Q:
3p
d3sdks_
S:
3q
d3sdku_
U:
3r
d3sdkv_
V:
3s
d3sdkw_
W:
3t
d3sdkx_
X:
3u
d3sdky_
Y:
3v
d3sdkz_
Z:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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all PFAM domains
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