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.
5L5J
Asym. Unit
Info
Asym.Unit (2.0 MB)
Biol.Unit 1, α-C (2.0 MB)
Biol.Unit 1 (2.0 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
YEAST 20S PROTEASOME WITH HUMAN BETA5I (1-138) AND HUMAN BETA6 (97-111; 118-133) IN COMPLEX WITH EPOXYKETONE INHIBITOR 14
Authors
:
M. Groll, E. M. Huber
Date
:
28 May 16 (Deposition) - 09 Nov 16 (Release) - 14 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
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
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 (1x)
Keywords
:
Hydrolase-Hydrolase Inhibitor Complex, Proteasome, Mutant, Inhibitor, Binding Analysis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. M. Huber, W. Heinemeyer, G. De Bruin, H. S. Overkleeft, M. Groll
A Humanized Yeast Proteasome Identifies Unique Binding Mode Of Inhibitors For The Immunosubunit Beta 5I.
Embo J. V. 35 2602 2016
[
close entry info
]
Hetero Components
(4, 16)
Info
All Hetero Components
1a: ~{N}-[(2~{S})-1-[[(2~{S})-3-(4-MET... (6N5a)
1b: ~{N}-[(2~{S})-1-[[(2~{S})-3-(4-MET... (6N5b)
1c: ~{N}-[(2~{S})-1-[[(2~{S})-3-(4-MET... (6N5c)
1d: ~{N}-[(2~{S})-1-[[(2~{S})-3-(4-MET... (6N5d)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
3b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6N5
4
Ligand/Ion
~{N}-[(2~{S})-1-[[(2~{S})-3-(4-METHOXYPHENYL)-1-[[(2~{S},3~{S},4~{R})-4-METHYL-3,5-BIS(OXIDANYL)-1-PHENYL-PENTAN-2-YL]AMINO]-1-OXIDANYLIDENE-PROPAN-2-YL]AMINO]-1-OXIDANYLIDENE-PROPAN-2-YL]-1-METHYL-5~{H}-INDENE-2-CARBOXAMIDE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
MG
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(18, 18)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR G:8 , TYR G:119 , ARG G:122 , ALA G:123 , MET G:125
binding site for residue MG G 301
02
AC2
SOFTWARE
ARG G:111 , ASN G:114 , TYR H:69
binding site for residue CL G 302
03
AC3
SOFTWARE
THR H:1 , ARG H:19 , SER H:20 , THR H:21 , GLN H:22 , CYS H:31 , GLY H:45 , GLY H:47 , THR H:48 , ALA H:49 , THR H:52 , GLY H:168 , MES H:302 , ASP I:124 , LEU I:125
binding site for residue 6N5 H 301
04
AC4
SOFTWARE
GLY H:47 , GLY H:128 , 6N5 H:301
binding site for residue MES H 302
05
AC5
SOFTWARE
ALA I:174 , ASP I:177 , SER I:180 , ASP I:204
binding site for residue MG I 301
06
AC6
SOFTWARE
ASP I:204 , ARG Y:19 , ALA Y:164 , ASP Y:167 , ALA Y:168 , SER Y:170
binding site for residue MG I 302
07
AC7
SOFTWARE
GLN J:118 , THR J:124
binding site for residue MG J 201
08
AC8
SOFTWARE
THR K:1 , ARG K:19 , ALA K:20 , SER K:21 , LYS K:33 , GLY K:47 , ALA K:49 , TYR K:169 , TYR L:108 , ASP L:126
binding site for residue 6N5 K 301
09
AC9
SOFTWARE
ARG K:19 , ALA K:164 , ASP K:167 , ALA K:168 , SER K:170 , ASP W:204
binding site for residue MG K 302
10
AD1
SOFTWARE
ASP L:222 , ILE V:163 , TRP V:164 , ASP V:166 , SER V:169
binding site for residue MG L 301
11
AD2
SOFTWARE
ARG N:19 , ILE N:163 , ASP N:166 , SER N:169 , LEU a:34
binding site for residue MG N 201
12
AD3
SOFTWARE
ARG U:111 , ASN U:114 , TYR V:69
binding site for residue CL U 301
13
AD4
SOFTWARE
GLY Y:47 , GLY Y:129 , SER Y:130 , 6N5 Y:301
binding site for residue MES Y 302
14
AD5
SOFTWARE
THR Z:192 , HIS Z:195 , ILE Z:196 , VAL Z:198 , ASP Z:222
binding site for residue MG Z 301
15
AD6
SOFTWARE
THR V:2 , ILE V:3 , ASP V:17 , ARG V:19 , SER V:20 , THR V:21 , GLN V:22 , CYS V:31 , LYS V:33 , GLY V:45 , GLY V:47 , THR V:48 , ALA V:49 , THR V:52 , GLY V:128 , SER V:129 , GLY V:130 , GLY V:168 , SER V:169 , HOH V:403 , ASP W:124 , LEU W:125 , ILE W:126
binding site for Di-peptide 6N5 V 301 and THR V 1
16
AD7
SOFTWARE
THR V:2 , ILE V:3 , ASP V:17 , ARG V:19 , SER V:20 , THR V:21 , GLN V:22 , CYS V:31 , LYS V:33 , GLY V:45 , GLY V:47 , THR V:48 , ALA V:49 , THR V:52 , GLY V:128 , SER V:129 , GLY V:130 , GLY V:168 , SER V:169 , HOH V:403 , ASP W:124 , LEU W:125 , ILE W:126
binding site for Di-peptide 6N5 V 301 and THR V 1
17
AD8
SOFTWARE
THR Y:2 , THR Y:3 , ASP Y:17 , ARG Y:19 , ALA Y:20 , SER Y:21 , LYS Y:33 , MET Y:45 , GLY Y:47 , ALA Y:49 , GLY Y:129 , SER Y:130 , GLY Y:131 , TYR Y:169 , SER Y:170 , MES Y:302 , TYR Z:108 , ASP Z:126 , PRO Z:127
binding site for Di-peptide 6N5 Y 301 and THR Y 1
18
AD9
SOFTWARE
THR Y:2 , THR Y:3 , ASP Y:17 , ARG Y:19 , ALA Y:20 , SER Y:21 , LYS Y:33 , MET Y:45 , GLY Y:47 , ALA Y:49 , GLY Y:129 , SER Y:130 , GLY Y:131 , TYR Y:169 , SER Y:170 , MES Y:302 , TYR Z:108 , ASP Z:126 , PRO Z:127
binding site for Di-peptide 6N5 Y 301 and THR Y 1
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (2.0 MB)
Header - Asym.Unit
Biol.Unit 1 (2.0 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
5L5J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
