PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3MG0
Asym. Unit
Info
Asym.Unit (1022 KB)
Biol.Unit 1 (1014 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF YEAST 20S PROTEASOME WITH BORTEZOMIB
Authors
:
M. D. Sintchak
Date
:
05 Apr 10 (Deposition) - 18 May 11 (Release) - 10 May 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.68
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
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Blackburn, K. M. Gigstad, P. Hales, K. Garcia, M. Jones, F. J. Bruzzese, C. Barrett, J. X. Liu, T. A. Soucy, D. S. Sappal, N. Bump, E. J. Olhava, P. Fleming, L. R. Dick, C. Tsu, M. D. Sintchak, J. L. Blank
Characterization Of A New Series Of Non-Covalent Proteasome Inhibitors With Exquisite Potency And Selectivity For The 20S Beta5-Subunit.
Biochem. J. V. 430 461 2010
[
close entry info
]
Hetero Components
(1, 6)
Info
All Hetero Components
1a: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHY... (BO2a)
1b: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHY... (BO2b)
1c: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHY... (BO2c)
1d: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHY... (BO2d)
1e: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHY... (BO2e)
1f: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHY... (BO2f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BO2
6
Ligand/Ion
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR H:1 , SER H:20 , THR H:21 , GLN H:22 , ALA H:46 , GLY H:47 , ALA H:49 , ASP I:114 , HOH I:1023
BINDING SITE FOR RESIDUE BO2 H 1400
2
AC2
SOFTWARE
THR K:1 , ALA K:20 , THR K:21 , ALA K:27 , LYS K:33 , ALA K:46 , GLY K:47 , ALA K:49 , ASP L:114
BINDING SITE FOR RESIDUE BO2 K 1402
3
AC3
SOFTWARE
HIS H:114 , SER H:118 , THR N:1 , THR N:20 , THR N:21 , THR N:22 , LYS N:33 , ARG N:45 , SER N:46 , GLY N:47 , ALA N:49 , HOH N:880
BINDING SITE FOR RESIDUE BO2 N 1404
4
AC4
SOFTWARE
THR V:1 , SER V:20 , THR V:21 , GLN V:22 , ALA V:46 , GLY V:47 , ALA V:49 , ASP W:114 , HOH W:1122
BINDING SITE FOR RESIDUE BO2 V 1401
5
AC5
SOFTWARE
THR Y:1 , ARG Y:19 , ALA Y:20 , THR Y:21 , ALA Y:27 , LYS Y:33 , ALA Y:46 , GLY Y:47 , ALA Y:49 , ASP Z:114
BINDING SITE FOR RESIDUE BO2 Y 1403
6
AC6
SOFTWARE
THR 2:1 , THR 2:20 , THR 2:21 , THR 2:22 , LYS 2:33 , ARG 2:45 , SER 2:46 , GLY 2:47 , ALA 2:49 , HOH 2:316 , HOH 2:1136 , HIS V:114 , SER V:118
BINDING SITE FOR RESIDUE BO2 2 1405
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 48)
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
PSA3_YEAST
6-28
2
B:8-30
P:8-30
PSA7_YEAST
8-30
2
F:8-30
T: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:4-239 (gaps) | P:4-239 (gaps))
Exon 7.1 (D:9-244 (gaps) | R:9-244 (gaps))
Exon 8.1 (2:1-3 | N:1-3)
Exon 8.2 (2:3-18J (gaps) | N:3-18J (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:5-241 (gaps) | T:5-241 (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)
225
225
2.1
YER012W
1
YER012W.1
V:177834-178430
597
PSB4_YEAST
1-198
198
2
J:-1-193 (gaps)
X:-1-193 (gaps)
200
200
3.1
YER094C
1
YER094C.1
V:349342-348725
618
PSB3_YEAST
1-205
205
2
I:-8-194 (gaps)
W:-8-194 (gaps)
208
208
4.1
YFR050C
1
YFR050C.1
VI:249853-249053
801
PSB7_YEAST
1-266
266
2
1:-8-211 (gaps)
M:-8-211 (gaps)
238
238
5.1
YGL011C
1
YGL011C.1
VII:475252-474494
759
PSA1_YEAST
1-252
252
2
G:6-240 (gaps)
U:6-240 (gaps)
247
247
6.1
YGR135W
1
YGR135W.1
VII:761397-762173
777
PSA3_YEAST
1-258
258
2
B:4-239 (gaps)
P:4-239 (gaps)
250
250
7.1
YGR253C
1
YGR253C.1
VII:999145-998363
783
PSA5_YEAST
1-260
260
2
D:9-244 (gaps)
R:9-244 (gaps)
249
249
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
2:3-18J (gaps)
N:3-18J (gaps)
198
198
9.1
YML092C
1
YML092C.1
XIII:86739-85987
753
PSA2_YEAST
1-250
250
2
A:4-236 (gaps)
O:4-236 (gaps)
255
255
10.1
YMR314W
1
YMR314W.1
XIII:901708-902412
705
PSA6_YEAST
1-234
234
2
E:4-233 (gaps)
S:4-233 (gaps)
239
239
11.1
YOL038W
1
YOL038W.1
XV:255336-256100
765
PSA4_YEAST
1-254
254
2
C:7-243 (gaps)
Q:7-243 (gaps)
246
246
12.1
YOR157C
1
YOR157C.1
XV:631752-630967
786
PSB2_YEAST
1-261
261
2
H:1-223 (gaps)
V:1-223 (gaps)
225
225
13.1
YOR362C
1
YOR362C.1
XV:1018744-1017878
867
PSA7_YEAST
1-288
288
2
F:5-241 (gaps)
T:5-241 (gaps)
248
248
14.1
YPR103W
1
YPR103W.1
XVI:732347-733210
864
PSB5_YEAST
1-287
287
2
K:1-211 (gaps)
Y:1-211 (gaps)
214
214
[
close EXON info
]
SCOP Domains
(3, 28)
Info
All SCOP Domains
1a: SCOP_d3mg0g_ (G:)
1b: SCOP_d3mg0u_ (U:)
2a: SCOP_d3mg0a_ (A:)
2b: SCOP_d3mg0b_ (B:)
2c: SCOP_d3mg0c_ (C:)
2d: SCOP_d3mg0e_ (E:)
2e: SCOP_d3mg0f_ (F:)
2f: SCOP_d3mg0o_ (O:)
2g: SCOP_d3mg0p_ (P:)
2h: SCOP_d3mg0q_ (Q:)
2i: SCOP_d3mg0s_ (S:)
2j: SCOP_d3mg0t_ (T:)
3a: SCOP_d3mg01_ (1:)
3b: SCOP_d3mg02_ (2:)
3c: SCOP_d3mg0d_ (D:)
3d: SCOP_d3mg0h_ (H:)
3e: SCOP_d3mg0i_ (I:)
3f: SCOP_d3mg0j_ (J:)
3g: SCOP_d3mg0k_ (K:)
3h: SCOP_d3mg0l_ (L:)
3i: SCOP_d3mg0m_ (M:)
3j: SCOP_d3mg0n_ (N:)
3k: SCOP_d3mg0r_ (R:)
3l: SCOP_d3mg0v_ (V:)
3m: SCOP_d3mg0w_ (W:)
3n: SCOP_d3mg0x_ (X:)
3o: SCOP_d3mg0y_ (Y:)
3p: SCOP_d3mg0z_ (Z:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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: 4932]
(39)
1a
d3mg0g_
G:
1b
d3mg0u_
U:
Protein domain
:
Proteasome alpha subunit (non-catalytic)
(66)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(54)
2a
d3mg0a_
A:
2b
d3mg0b_
B:
2c
d3mg0c_
C:
2d
d3mg0e_
E:
2e
d3mg0f_
F:
2f
d3mg0o_
O:
2g
d3mg0p_
P:
2h
d3mg0q_
Q:
2i
d3mg0s_
S:
2j
d3mg0t_
T:
Protein domain
:
Proteasome beta subunit (catalytic)
(61)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(51)
3a
d3mg01_
1:
3b
d3mg02_
2:
3c
d3mg0d_
D:
3d
d3mg0h_
H:
3e
d3mg0i_
I:
3f
d3mg0j_
J:
3g
d3mg0k_
K:
3h
d3mg0l_
L:
3i
d3mg0m_
M:
3j
d3mg0n_
N:
3k
d3mg0r_
R:
3l
d3mg0v_
V:
3m
d3mg0w_
W:
3n
d3mg0x_
X:
3o
d3mg0y_
Y:
3p
d3mg0z_
Z:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Proteasome_3mg0O01 (O:31-215)
1b: PFAM_Proteasome_3mg0O02 (O:31-215)
1c: PFAM_Proteasome_3mg0R01 (R:31-215)
1d: PFAM_Proteasome_3mg0R02 (R:31-215)
1e: PFAM_Proteasome_3mg0W01 (W:-3-178)
1f: PFAM_Proteasome_3mg0W02 (W:-3-178)
1g: PFAM_Proteasome_3mg0Y01 (Y:1-178)
1h: PFAM_Proteasome_3mg0Y02 (Y:1-178)
2a: PFAM_Proteasome_A_N_3mg0O03 (O:8-30)
2b: PFAM_Proteasome_A_N_3mg0O04 (O:8-30)
2c: PFAM_Proteasome_A_N_3mg0R03 (R:9-30)
2d: PFAM_Proteasome_A_N_3mg0R04 (R:9-30)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NTN
(93)
Family
:
Proteasome
(36)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(13)
1a
Proteasome-3mg0O01
O:31-215
1b
Proteasome-3mg0O02
O:31-215
1c
Proteasome-3mg0R01
R:31-215
1d
Proteasome-3mg0R02
R:31-215
1e
Proteasome-3mg0W01
W:-3-178
1f
Proteasome-3mg0W02
W:-3-178
1g
Proteasome-3mg0Y01
Y:1-178
1h
Proteasome-3mg0Y02
Y:1-178
Clan
:
no clan defined [family: Proteasome_A_N]
(20)
Family
:
Proteasome_A_N
(20)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
2a
Proteasome_A_N-3mg0O03
O:8-30
2b
Proteasome_A_N-3mg0O04
O:8-30
2c
Proteasome_A_N-3mg0R03
R:9-30
2d
Proteasome_A_N-3mg0R04
R:9-30
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Chain V
Chain W
Chain X
Chain Y
Chain Z
Chain 1
Chain 2
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
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)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (1022 KB)
Header - Asym.Unit
Biol.Unit 1 (1014 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3MG0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
