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.
1FNT
Asym. Unit
Info
Asym.Unit (1.4 MB)
Biol.Unit 1, α-C (1.4 MB)
Biol.Unit 1 (1.4 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST IN COMPLEX WITH THE PROTEASOME ACTIVATOR PA26 FROM TRYPANOSOME BRUCEI AT 3.2 ANGSTROMS RESOLUTION
Authors
:
F. G. Whitby, E. Masters, L. Kramer, J. R. Knowlton, Y. Yao, C. C. Wang, C. P. Hill
Date
:
23 Aug 00 (Deposition) - 11 Apr 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
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,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p
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,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p (1x)
Keywords
:
Multicatalytic Proteinase, 20S Proteasome, Protein Degradation, Antigen Processing, Protease, Proteasome Activator, Cell Adhesion, Interferon Induction, Hydrolase/Hydrolase Activator Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. G. Whitby, E. I. Masters, L. Kramer, J. R. Knowlton, Y. Yao, C. C. Wang, C. P. Hill
Structural Basis For The Activation Of 20S Proteasomes By 11S Regulators.
Nature V. 408 115 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 14)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
1l: MAGNESIUM ION (MGl)
1m: MAGNESIUM ION (MGm)
1n: MAGNESIUM ION (MGn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
14
Ligand/Ion
MAGNESIUM ION
[
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
ILE I:163 , ASP I:166 , LEU I:167 , SER I:169 , ASP a:213
BINDING SITE FOR RESIDUE MG I 1001
02
AC2
SOFTWARE
ILE H:163 , ASP H:166 , SER H:169
BINDING SITE FOR RESIDUE MG H 1002
03
AC3
SOFTWARE
ALA L:165 , HIS L:166 , ARG L:167 , ASP L:168 , ALA L:169 , ASP X:196
BINDING SITE FOR RESIDUE MG L 1003
04
AC4
SOFTWARE
GLU E:105 , SER M:76 , SER M:79 , GLU M:107
BINDING SITE FOR RESIDUE MG M 1004
05
AC5
SOFTWARE
ALA J:166 , ASP J:169 , SER J:172 , ASP J:196
BINDING SITE FOR RESIDUE MG J 1005
06
AC6
SOFTWARE
GLY J:131 , THR J:132 , SER J:134
BINDING SITE FOR RESIDUE MG J 1006
07
AC7
SOFTWARE
SER G:12 , ASN G:126
BINDING SITE FOR RESIDUE MG G 1007
08
AC8
SOFTWARE
ASP M:213 , ILE W:163 , ASP W:166 , SER W:169
BINDING SITE FOR RESIDUE MG W 1008
09
AC9
SOFTWARE
ARG V:19 , ILE V:163 , ASP V:166 , GLY V:167 , SER V:169
BINDING SITE FOR RESIDUE MG V 1009
10
BC1
SOFTWARE
ASP J:196 , ALA Z:165 , ASP Z:168 , ALA Z:169 , SER Z:171
BINDING SITE FOR RESIDUE MG Z 1010
11
BC2
SOFTWARE
GLU S:105 , SER a:76 , SER a:79
BINDING SITE FOR RESIDUE MG A 1011
12
BC3
SOFTWARE
ALA X:166 , ASP X:169 , SER X:172 , ASP X:196
BINDING SITE FOR RESIDUE MG X 1012
13
BC4
SOFTWARE
GLY X:131 , SER X:134
BINDING SITE FOR RESIDUE MG X 1013
14
BC5
SOFTWARE
SER U:12 , ASN U:126
BINDING SITE FOR RESIDUE MG U 1014
[
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, 44)
Info
All PROSITE Patterns/Profiles
1: PROTEASOME_BETA_2 (K:-1-183,Y:-1-183,J:-1-181,X:-1-18...)
2: PROTEASOME_ALPHA_1 (B:5-27,P:5-27,F:6-28,T:6-28,C:6-28...)
3: PROTEASOME_BETA_1 (K:4-51,Y:4-51,J:4-50,X:4-50,H:4-51...)
4: PROTEASOME_ALPHA_2 (D:19-233,R:19-233,B:20-247,P:20-24...)
;
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
K:-1-183
Y:-1-183
PSB3_YEAST
9-190
2
J:-1-181
X:-1-181
PSB6_YEAST
28-226
2
M:-1-198
a:-1-198
PSB7_YEAST
41-233
2
N:-1-192
b:-1-192
2
PROTEASOME_ALPHA_1
PS00388
Proteasome alpha-type subunits signature.
PSA2_YEAST
5-27
2
B:5-27
P:5-27
PSA6_YEAST
6-28
2
F:6-28
T:6-28
PSA3_YEAST
6-28
2
C:6-28
Q:6-28
PSA5_YEAST
8-30
2
E:8-30
S:8-30
3
PROTEASOME_BETA_1
PS00854
Proteasome beta-type subunits signature.
PSB4_YEAST
5-52
2
K:4-51
Y:4-51
PSB3_YEAST
13-59
2
J:4-50
X:4-50
PSB1_YEAST
23-70
2
H:4-51
V:4-51
PSB6_YEAST
32-79
2
M:4-51
a:4-51
PSB2_YEAST
33-80
2
I:4-51
W:4-51
PSB7_YEAST
45-92
2
N:4-51
b:4-51
PSB5_YEAST
79-126
2
L:4-51
Z:4-51
4
PROTEASOME_ALPHA_2
PS51475
Proteasome alpha-type subunit profile.
PSA4_YEAST
19-233
2
D:19-233
R:19-233
PSA2_YEAST
20-247
2
B:20-247
P:20-247
PSA6_YEAST
21-234
2
F:21-234
T:21-234
PSA3_YEAST
21-239
2
C:21-239
Q:21-239
PSA5_YEAST
23-240
2
E:23-240
S:23-240
PSA7_YEAST
23-240
2
G:22-239
U:22-239
PSA1_YEAST
27-245
2
A:27-245
O:27-245
[
close PROSITE info
]
Exons
(15, 30)
Info
All Exons
Exon 1.1 (M:-9-213 | a:-9-213)
Exon 2.1 (K:-1-197 | Y:-1-197)
Exon 3.1 (J:-8-196 | X:-8-196)
Exon 4.1 (N:-8-225 | b:-8-225)
Exon 5.1 (A:15-252 | O:15-252)
Exon 6.1 (C:5-245 | Q:5-245)
Exon 7.1 (E:7-250 | S:7-250)
Exon 8.1 (H:1-3 | V:1-3)
Exon 8.2 (H:3-196 | V:3-196)
Exon 9.1 (B:4-250 | P:4-250)
Exon 10.1 (F:2-234 | T:2-234)
Exon 11.1 (D:5-243 | R:5-243)
Exon 12.1 (I:1-222 | W:1-222)
Exon 13.1 (G:8-247 | U:8-247)
Exon 14.1 (L:1-212 | Z:1-212)
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
M:-9-213
a:-9-213
222
222
2.1
YER012W
1
YER012W.1
V:177834-178430
597
PSB4_YEAST
1-198
198
2
K:-1-197
Y:-1-197
198
198
3.1
YER094C
1
YER094C.1
V:349342-348725
618
PSB3_YEAST
1-205
205
2
J:-8-196
X:-8-196
204
204
4.1
YFR050C
1
YFR050C.1
VI:249853-249053
801
PSB7_YEAST
1-266
266
2
N:-8-225
b:-8-225
233
233
5.1
YGL011C
1
YGL011C.1
VII:475252-474494
759
PSA1_YEAST
1-252
252
2
A:15-252
O:15-252
238
238
6.1
YGR135W
1
YGR135W.1
VII:761397-762173
777
PSA3_YEAST
1-258
258
2
C:5-245
Q:5-245
241
241
7.1
YGR253C
1
YGR253C.1
VII:999145-998363
783
PSA5_YEAST
1-260
260
2
E:7-250
S:7-250
244
244
8.1
YJL001W
1
YJL001W.1
X:435156-435220
65
PSB1_YEAST
1-22
22
2
H:1-3
V:1-3
3
3
8.2
YJL001W
2
YJL001W.2
X:435337-435919
583
PSB1_YEAST
22-215
194
2
H:3-196
V:3-196
194
194
9.1
YML092C
1
YML092C.1
XIII:86739-85987
753
PSA2_YEAST
1-250
250
2
B:4-250
P:4-250
247
247
10.1
YMR314W
1
YMR314W.1
XIII:901708-902412
705
PSA6_YEAST
1-234
234
2
F:2-234
T:2-234
233
233
11.1
YOL038W
1
YOL038W.1
XV:255336-256100
765
PSA4_YEAST
1-254
254
2
D:5-243
R:5-243
239
239
12.1
YOR157C
1
YOR157C.1
XV:631752-630967
786
PSB2_YEAST
1-261
261
2
I:1-222
W:1-222
222
222
13.1
YOR362C
1
YOR362C.1
XV:1018744-1017878
867
PSA7_YEAST
1-288
288
2
G:8-247
U:8-247
240
240
14.1
YPR103W
1
YPR103W.1
XVI:732347-733210
864
PSB5_YEAST
1-287
287
2
L:1-212
Z:1-212
212
212
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 42)
Info
all CATH domains
1a: CATH_1fntM00 (M:-9-213)
1b: CATH_1fntF00 (F:2-234)
1c: CATH_1fntT00 (T:2-234)
1d: CATH_1fntL00 (L:1-212)
1e: CATH_1fntZ00 (Z:1-212)
1f: CATH_1fntD00 (D:5-243)
1g: CATH_1fntR00 (R:5-243)
1h: CATH_1fntA00 (A:15-252)
1i: CATH_1fntO00 (O:15-252)
1j: CATH_1fntC00 (C:5-245)
1k: CATH_1fntQ00 (Q:5-245)
1l: CATH_1fnta00 (a:-9-213)
1m: CATH_1fntG00 (G:8-247)
1n: CATH_1fntU00 (U:8-247)
1o: CATH_1fntH00 (H:1-196)
1p: CATH_1fntV00 (V:1-196)
1q: CATH_1fntJ00 (J:-8-196)
1r: CATH_1fntX00 (X:-8-196)
1s: CATH_1fntB00 (B:4-250)
1t: CATH_1fntP00 (P:4-250)
1u: CATH_1fntK00 (K:-1-197)
1v: CATH_1fntY00 (Y:-1-197)
1w: CATH_1fntI00 (I:1-222)
1x: CATH_1fntW00 (W:1-222)
1y: CATH_1fntE00 (E:7-250)
1z: CATH_1fntS00 (S:7-250)
1aa: CATH_1fntN00 (N:-8-225)
1ab: CATH_1fntb00 (b:-8-225)
2a: CATH_1fntc01 (c:6-221)
2b: CATH_1fntd01 (d:6-221)
2c: CATH_1fntm01 (m:6-221)
2d: CATH_1fntn01 (n:6-221)
2e: CATH_1fnto01 (o:6-221)
2f: CATH_1fntp01 (p:6-221)
2g: CATH_1fnte01 (e:6-221)
2h: CATH_1fntf01 (f:6-221)
2i: CATH_1fntg01 (g:6-221)
2j: CATH_1fnth01 (h:6-221)
2k: CATH_1fnti01 (i:6-221)
2l: CATH_1fntj01 (j:6-221)
2m: CATH_1fntk01 (k:6-221)
2n: CATH_1fntl01 (l:6-221)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(128)
Homologous Superfamily
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(124)
Baker's yeast (Saccharomyces cerevisiae)
(14)
1a
1fntM00
M:-9-213
1b
1fntF00
F:2-234
1c
1fntT00
T:2-234
1d
1fntL00
L:1-212
1e
1fntZ00
Z:1-212
1f
1fntD00
D:5-243
1g
1fntR00
R:5-243
1h
1fntA00
A:15-252
1i
1fntO00
O:15-252
1j
1fntC00
C:5-245
1k
1fntQ00
Q:5-245
1l
1fnta00
a:-9-213
1m
1fntG00
G:8-247
1n
1fntU00
U:8-247
1o
1fntH00
H:1-196
1p
1fntV00
V:1-196
1q
1fntJ00
J:-8-196
1r
1fntX00
X:-8-196
1s
1fntB00
B:4-250
1t
1fntP00
P:4-250
1u
1fntK00
K:-1-197
1v
1fntY00
Y:-1-197
1w
1fntI00
I:1-222
1x
1fntW00
W:1-222
1y
1fntE00
E:7-250
1z
1fntS00
S:7-250
1aa
1fntN00
N:-8-225
1ab
1fntb00
b:-8-225
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.180, no name defined]
(10)
Baker's yeast (Saccharomyces cerevisiae)
(2)
2a
1fntc01
c:6-221
2b
1fntd01
d:6-221
2c
1fntm01
m:6-221
2d
1fntn01
n:6-221
2e
1fnto01
o:6-221
2f
1fntp01
p:6-221
2g
1fnte01
e:6-221
2h
1fntf01
f:6-221
2i
1fntg01
g:6-221
2j
1fnth01
h:6-221
2k
1fnti01
i:6-221
2l
1fntj01
j:6-221
2m
1fntk01
k:6-221
2n
1fntl01
l:6-221
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 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
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 (1.4 MB)
Header - Asym.Unit
Biol.Unit 1 (1.4 MB)
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
1FNT
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
