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.
2Z6W
Asym. Unit
Info
Asym.Unit (146 KB)
Biol.Unit 1 (70 KB)
Biol.Unit 2 (72 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 HUMAN CYCLOPHILIN D IN COMPLEX WITH CYCLOSPORIN A
Authors
:
K. Kajitani, M. Fujihashi, Y. Kobayashi, S. Shimizu, Y. Tsujimoto, K. M
Date
:
09 Aug 07 (Deposition) - 29 Apr 08 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
0.96
Chains
:
Asym. Unit : A,B,M,N
Biol. Unit 1: A,M (1x)
Biol. Unit 2: B,N (1x)
Keywords
:
Isomerase-Immunosuppressant Complex, Cyclophilin-Cyclosporin Complex, Cyclosporin A, Immunosuppressant, Cyclophilin D
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Kajitani, M. Fujihashi, Y. Kobayashi, S. Shimizu, Y. Tsujimoto, K. Miki
Crystal Structure Of Human Cyclophilin D In Complex With It Inhibitor, Cyclosporin A At 0. 96-A Resolution.
Proteins V. 70 1635 2008
[
close entry info
]
Hetero Components
(7, 19)
Info
All Hetero Components
1a: ALPHA-AMINOBUTYRIC ACID (ABAa)
1b: ALPHA-AMINOBUTYRIC ACID (ABAb)
2a: 4-METHYL-4-[(E)-2-BUTENYL]-4,N-MET... (BMTa)
2b: 4-METHYL-4-[(E)-2-BUTENYL]-4,N-MET... (BMTb)
3a: CITRIC ACID (CITa)
4a: D-ALANINE (DALa)
4b: D-ALANINE (DALb)
5a: N-METHYLLEUCINE (MLEa)
5b: N-METHYLLEUCINE (MLEb)
5c: N-METHYLLEUCINE (MLEc)
5d: N-METHYLLEUCINE (MLEd)
5e: N-METHYLLEUCINE (MLEe)
5f: N-METHYLLEUCINE (MLEf)
5g: N-METHYLLEUCINE (MLEg)
5h: N-METHYLLEUCINE (MLEh)
6a: N-METHYLVALINE (MVAa)
6b: N-METHYLVALINE (MVAb)
7a: SARCOSINE (SARa)
7b: SARCOSINE (SARb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ABA
2
Mod. Amino Acid
ALPHA-AMINOBUTYRIC ACID
2
BMT
2
Mod. Amino Acid
4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
3
CIT
1
Ligand/Ion
CITRIC ACID
4
DAL
2
Mod. Amino Acid
D-ALANINE
5
MLE
8
Mod. Amino Acid
N-METHYLLEUCINE
6
MVA
2
Mod. Amino Acid
N-METHYLVALINE
7
SAR
2
Mod. Amino Acid
SARCOSINE
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:50 , SER A:51 , THR A:52 , HIS A:70 , GLY A:80 , SER A:81 , ARG A:82 , LYS A:155 , HOH A:2149 , HOH A:2257 , HOH A:2258
BINDING SITE FOR RESIDUE CIT A 3001
2
AC2
SOFTWARE
ARG A:55 , PHE A:60 , GLN A:63 , GLY A:72 , ALA A:101 , ASN A:102 , ALA A:103 , GLN A:111 , PHE A:113 , TRP A:121 , HIS A:126 , HOH A:2135 , LEU B:5 , SER B:81 , ALA B:103 , GLU B:134 , LEU B:164 , HOH B:2161 , HOH B:2199 , HOH B:2244 , HOH M:2001 , HOH M:2002 , HOH M:2003 , HOH M:2004 , HOH M:2005 , HOH M:2006 , HOH M:2007 , HOH M:2008 , HOH M:2009 , HOH M:2010
BINDING SITE FOR CHAIN M OF CYCLOSPORIN A
3
AC3
SOFTWARE
GLY A:104 , HOH A:2197 , ARG B:37 , GLU B:43 , ARG B:55 , PHE B:60 , GLN B:63 , GLY B:72 , ALA B:101 , ASN B:102 , GLN B:111 , PHE B:113 , TRP B:121 , HIS B:126 , GLN B:163 , LEU B:164 , SER B:165 , HOH B:2110 , HOH B:2124 , HOH B:2218 , HOH N:2001 , HOH N:2005 , HOH N:2006 , HOH N:2007 , HOH N:2008
BINDING SITE FOR CHAIN N OF CYCLOSPORIN A
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: CSA_PPIASE_2 (A:7-163,B:7-163)
2: CSA_PPIASE_1 (A:48-65,B:48-65)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CSA_PPIASE_2
PS50072
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.
PPIF_HUMAN
49-205
2
A:7-163
B:7-163
2
CSA_PPIASE_1
PS00170
Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.
PPIF_HUMAN
90-107
2
A:48-65
B:48-65
[
close PROSITE info
]
Exons
(6, 12)
Info
All Exons
Exon 1.1b (A:2-23 | B:2-23)
Exon 1.2 (A:24-34 | B:24-34)
Exon 1.3a (A:34-63 | B:34-63)
Exon 1.4a (A:64-96 | B:64-96)
Exon 1.5 (A:96-121 | B:96-121)
Exon 1.6c (A:121-165 | B:121-165)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.2
3: Boundary 1.2/1.3a
4: Boundary 1.3a/1.4a
5: Boundary 1.4a/1.5
6: Boundary 1.5/1.6c
7: Boundary 1.6c/-
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
1.1b
ENST00000225174
1b
ENSE00001554110
chr10:
81107234-81107499
266
PPIF_HUMAN
1-65
65
2
A:2-23
B:2-23
22
22
1.2
ENST00000225174
2
ENSE00000998348
chr10:
81108832-81108862
31
PPIF_HUMAN
66-76
11
2
A:24-34
B:24-34
11
11
1.3a
ENST00000225174
3a
ENSE00000710825
chr10:
81109421-81109509
89
PPIF_HUMAN
76-105
30
2
A:34-63
B:34-63
30
30
1.4a
ENST00000225174
4a
ENSE00000429803
chr10:
81111243-81111339
97
PPIF_HUMAN
106-138
33
2
A:64-96
B:64-96
33
33
1.5
ENST00000225174
5
ENSE00000710835
chr10:
81112073-81112148
76
PPIF_HUMAN
138-163
26
2
A:96-121
B:96-121
26
26
1.6c
ENST00000225174
6c
ENSE00001136191
chr10:
81113463-81115093
1631
PPIF_HUMAN
163-207
45
2
A:121-165
B:121-165
45
45
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2z6wa_ (A:)
1b: SCOP_d2z6wb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cyclophilin-like
(169)
Superfamily
:
Cyclophilin-like
(169)
Family
:
Cyclophilin (peptidylprolyl isomerase)
(160)
Protein domain
:
Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
(25)
Human (Homo sapiens) [TaxId: 9606]
(25)
1a
d2z6wa_
A:
1b
d2z6wb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Pro_isomerase_2z6wB01 (B:7-163)
1b: PFAM_Pro_isomerase_2z6wB02 (B:7-163)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cyclophil-like
(65)
Family
:
Pro_isomerase
(53)
Homo sapiens (Human)
(42)
1a
Pro_isomerase-2z6wB01
B:7-163
1b
Pro_isomerase-2z6wB02
B:7-163
[
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 M
Chain N
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 (146 KB)
Header - Asym.Unit
Biol.Unit 1 (70 KB)
Header - Biol.Unit 1
Biol.Unit 2 (72 KB)
Header - Biol.Unit 2
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
2Z6W
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help