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.
2JK7
Asym. Unit
Info
Asym.Unit (24 KB)
Biol.Unit 1 (19 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
XIAP BIR3 BOUND TO A SMAC MIMETIC
Authors
:
N. G. Saito, J. L. Meagher, J. A. Stuckey
Date
:
21 Aug 08 (Deposition) - 04 Nov 08 (Release) - 09 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.82
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Zinc-Finger, Polymorphism, Smac Mimetic, Metal-Binding, Bir3, Zinc, Ligase, Apoptosis, Cytoplasm, X-Linked Inhibitor Of Apoptosis, Ubl Conjugation Pathway, Thiol Protease Inhibitor, Phosphoprotein, Ubl Conjugation, Protease Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Sun, J. A. Stuckey, Z. Nikolovska-Coleska, D. Qin, J. L. Meagher, S. Qiu, J. Lu, C. Yang, N. G. Saito, S. Wang
Structure-Based Design, Synthesis, Evaluation, And Crystallographic Studies Of Conformationally Constrained Smac Mimetics As Inhibitors Of The X- Linked Inhibitor Of Apoptosis Protein (Xiap).
J. Med. Chem. V. 51 7169 2008
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: (3S,6S,7Z,10AS)-N-(DIPHENYLMETHYL)... (BI6a)
2a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BI6
1
Ligand/Ion
(3S,6S,7Z,10AS)-N-(DIPHENYLMETHYL)-6-{[(2S)-2-(METHYLIDENEAMINO)BUTANOYL]AMINO}-5-OXO-1,2,3,5,6,9,10,10A-OCTAHYDROPYRROLO[1,2-A]AZOCINE-3-CARBOXAMIDE
2
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:297 , VAL A:298 , GLY A:306 , LEU A:307 , THR A:308 , ASP A:309 , TRP A:310 , LYS A:311 , GLU A:314 , TRP A:323 , TYR A:324 , HOH A:2037
BINDING SITE FOR RESIDUE BI6 A1346
2
AC2
SOFTWARE
CYS A:300 , CYS A:303 , HIS A:320 , CYS A:327
BINDING SITE FOR RESIDUE ZN A1347
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: BIR_REPEAT_1 (-|-|A:265-330)
2: BIR_REPEAT_2 (-|-|A:268-331)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BIR_REPEAT_1
PS01282
BIR repeat.
XIAP_HUMAN
26-93
163-230
265-330
1
-
-
A:265-330
2
BIR_REPEAT_2
PS50143
BIR repeat profile.
XIAP_HUMAN
29-94
166-231
268-331
1
-
-
A:268-331
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.3c (A:250-293)
Exon 1.4b (A:293-326)
Exon 1.5b (A:326-346)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2a/1.3c
2: Boundary 1.3c/1.4b
3: Boundary 1.4b/1.5b
4: Boundary 1.5b/1.6
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
1.2a
ENST00000371199
2a
ENSE00001810722
X:122993877-122994143
267
XIAP_HUMAN
-
0
0
-
-
1.3c
ENST00000371199
3c
ENSE00002176074
X:123019481-123020389
909
XIAP_HUMAN
1-293
293
1
A:250-293
44
1.4b
ENST00000371199
4b
ENSE00001649641
X:123022469-123022568
100
XIAP_HUMAN
293-326
34
1
A:293-326
34
1.5b
ENST00000371199
5b
ENSE00001630752
X:123025088-123025166
79
XIAP_HUMAN
326-352
27
1
A:326-346
21
1.6
ENST00000371199
6
ENSE00001714518
X:123026581-123026623
43
XIAP_HUMAN
353-367
15
0
-
-
1.7b
ENST00000371199
7b
ENSE00001653318
X:123034343-123034543
201
XIAP_HUMAN
367-434
68
0
-
-
1.8e
ENST00000371199
8e
ENSE00001454620
X:123040838-123047829
6992
XIAP_HUMAN
434-497
64
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2jk7a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Inhibitor of apoptosis (IAP) repeat
(71)
Superfamily
:
Inhibitor of apoptosis (IAP) repeat
(71)
Family
:
Inhibitor of apoptosis (IAP) repeat
(70)
Protein domain
:
BIR domains of XIAP
(15)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d2jk7a_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2jk7A00 (A:250-346)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
(42)
Homologous Superfamily
:
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
(42)
Human (Homo sapiens)
(35)
1a
2jk7A00
A:250-346
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_BIR_2jk7A01 (A:268-331)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
BIR-like
(25)
Family
:
BIR
(25)
Homo sapiens (Human)
(24)
1a
BIR-2jk7A01
A:268-331
[
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
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 (24 KB)
Header - Asym.Unit
Biol.Unit 1 (19 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
2JK7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help