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.
2PBK
Asym. Unit
Info
Asym.Unit (92 KB)
Biol.Unit 1 (85 KB)
(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 KSHV PROTEASE IN COMPLEX WITH HEXAPEPTIDE PHOSPHONATE INHIBITOR
Authors
:
A. Lazic, D. H. Goetz
Date
:
28 Mar 07 (Deposition) - 25 Dec 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.73
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Kshv, Kshv Protease, Herpesvirus Protease, Viral Protease, Viral Protein, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Lazic, D. H. Goetz, A. M. Nomura, A. B. Marnett, C. S. Craik
Substrate Modulation Of Enzyme Activity In The Herpesvirus Protease Family.
J. Mol. Biol. V. 373 913 2007
[
close entry info
]
Hetero Components
(4, 9)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
3a: [(1R)-1-AMINOETHYL]PHOSPHONIC ACID (GG7a)
3b: [(1R)-1-AMINOETHYL]PHOSPHONIC ACID (GG7b)
4a: 3-METHYL-L-VALINE (TBGa)
4b: 3-METHYL-L-VALINE (TBGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
2
Mod. Amino Acid
ACETYL GROUP
2
ACT
3
Ligand/Ion
ACETATE ION
3
GG7
2
Mod. Amino Acid
[(1R)-1-AMINOETHYL]PHOSPHONIC ACID
4
TBG
2
Mod. Amino Acid
3-METHYL-L-VALINE
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:12 , VAL A:14 , LEU A:25 , PRO A:27 , GLN A:60 , GLY A:64 , ILE A:65 , HOH A:643
BINDING SITE FOR RESIDUE ACT A 601
2
AC2
SOFTWARE
GLU A:100 , PRO A:101 , LEU A:102 , LEU A:103 , HIS A:152
BINDING SITE FOR RESIDUE ACT A 602
3
AC3
SOFTWARE
PRO B:39 , SER B:185 , HOH B:813 , HOH B:819
BINDING SITE FOR RESIDUE ACT B 603
4
AC4
SOFTWARE
GLU B:22 , HIS B:46 , SER B:114 , LEU B:115 , SER B:116 , SER B:117 , ILE B:118 , HIS B:119 , ARG B:121 , GLU B:122 , SER B:128 , GLY B:129 , PRO B:130 , GLN B:133 , GLY B:141 , ARG B:142 , ARG B:143 , HOH B:654 , HOH C:8 , HOH C:9 , HOH C:10 , HOH C:11 , HOH C:12 , HOH C:13 , HOH C:14 , HOH C:15 , HOH C:17
BINDING SITE FOR CHAIN C OF HEXAPEPTIDE PHOSPHONATE INHIBITOR
5
AC5
SOFTWARE
GLU A:22 , HIS A:46 , SER A:114 , LEU A:115 , SER A:116 , SER A:117 , ILE A:118 , HIS A:119 , GLU A:122 , PRO A:130 , GLY A:141 , ARG A:142 , ARG A:143 , HOH A:606 , HOH A:754 , HOH D:8 , HOH D:9 , HOH D:10 , HOH D:11 , HOH D:12 , HOH D:13
BINDING SITE FOR CHAIN D OF HEXAPEPTIDE PHOSPHONATE INHIBITOR
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2pbka_ (A:)
1b: SCOP_d2pbkb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Herpes virus serine proteinase, assemblin
(20)
Superfamily
:
Herpes virus serine proteinase, assemblin
(20)
Family
:
Herpes virus serine proteinase, assemblin
(20)
Protein domain
:
KSHV protease
(2)
Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]
(2)
1a
d2pbka_
A:
1b
d2pbkb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2pbkB00 (B:3-230)
1b: CATH_2pbkA00 (A:3-230)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
Serine Protease, Human Cytomegalovirus Protease; Chain A
(20)
Homologous Superfamily
:
Serine Protease, Human Cytomegalovirus Protease; Chain A
(20)
Human herpesvirus 8. Organism_taxid: 37296. Strain: 8.
(1)
1a
2pbkB00
B:3-230
1b
2pbkA00
A:3-230
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_S21_2pbkB01 (B:22-230)
1b: PFAM_Peptidase_S21_2pbkB02 (B:22-230)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_SH
(1)
Family
:
Peptidase_S21
(1)
Human herpesvirus 8 (HHV-8) (Kaposis sarcoma-associated herpesvirus)
(1)
1a
Peptidase_S21-2pbkB01
B:22-230
1b
Peptidase_S21-2pbkB02
B:22-230
[
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
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 (92 KB)
Header - Asym.Unit
Biol.Unit 1 (85 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
2PBK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
