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.
1B5F
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (120 KB)
Biol.Unit 2 (62 KB)
Biol.Unit 3 (62 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.
Authors
:
C. Frazao, I. Bento, M. A. Carrondo
Date
:
06 Jan 99 (Deposition) - 13 Jan 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Keywords
:
Hydrolase, Aspartic Proteinase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Frazao, I. Bento, J. Costa, C. M. Soares, P. Verissimo, C. Faro, E. Pires, J. Cooper, M. A. Carrondo
Crystal Structure Of Cardosin A, A Glycosylated And Arg-Gly-Asp-Containing Aspartic Proteinase From The Flowers Of Cynara Cardunculus L.
J. Biol. Chem. V. 274 27694 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 19)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
2c: ALPHA-L-FUCOSE (FUCc)
2d: ALPHA-L-FUCOSE (FUCd)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
FUC
4
Ligand/Ion
ALPHA-L-FUCOSE
3
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: 1 (AUTHOR)
02: 2 (AUTHOR)
03: 3 (AUTHOR)
04: 4 (AUTHOR)
05: 5 (AUTHOR)
06: 6 (AUTHOR)
07: AC1 (SOFTWARE)
08: AC2 (SOFTWARE)
09: AC3 (SOFTWARE)
10: AC4 (SOFTWARE)
11: AC5 (SOFTWARE)
12: AC6 (SOFTWARE)
13: AC7 (SOFTWARE)
14: AC8 (SOFTWARE)
15: AC9 (SOFTWARE)
16: BC1 (SOFTWARE)
17: BC2 (SOFTWARE)
18: BC3 (SOFTWARE)
19: BC4 (SOFTWARE)
20: BC5 (SOFTWARE)
21: BC6 (SOFTWARE)
22: BC7 (SOFTWARE)
23: BC8 (SOFTWARE)
24: BC9 (SOFTWARE)
25: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
1
AUTHOR
ASP A:32 , ASP A:215
ASPARTIC PROTEINASE CATALYTIC SITE WATER 1014 ASSOCIATED TO CHAIN A CATALYTIC SITE WATER 1035 ASSOCIATED TO CHAIN C CATALYTIC SITE
02
2
AUTHOR
ASN A:67
N-GLYCOSYLATION SITE ON CHAIN A, ASN67: (A1->3)- MAN405 | ASN67-NAG401-(B1->4)-NAG403-(B1->4)-MAN404 | (A1->3) FUC402
03
3
AUTHOR
ASN B:257
N-GLYCOSYLATION SITE ON CHAIN B, ASN257: ASN257- NAG501-(B1->4)-NAG503-(B1->4)-MAN504 | (A1->3)-FUC502
04
4
AUTHOR
ASP C:32 , ASP C:215
N-GLYCOSYLATION SITE ON CHAIN C, ASN67: (A1->3)- MAN405 | ASN67-NAG401-(B1->4)-NAG403-(B1->4)-MAN404 | | (A1->3)- FUC402 (A1->6)-MAN406
05
5
AUTHOR
ASN C:67
N-GLYCOSYLATION SITE ON CHAIN D, ASN257: ASN257- NAG501-(B1->4)-NAG503-(B1->4)-MAN504 | (A1->3)-FUC502
06
6
AUTHOR
ASN D:257
NULL
07
AC1
SOFTWARE
ASN A:67 , ASP A:100 , ILE A:132 , SER A:133 , FUC A:402 , NAG A:403
BINDING SITE FOR RESIDUE NAG A 401
08
AC2
SOFTWARE
NAG A:401 , NAG A:403
BINDING SITE FOR RESIDUE FUC A 402
09
AC3
SOFTWARE
GLN A:126 , ILE A:132 , NAG A:401 , FUC A:402 , BMA A:404 , HOH A:1080
BINDING SITE FOR RESIDUE NAG A 403
10
AC4
SOFTWARE
GLN A:126 , NAG A:403 , MAN A:405 , HOH A:1066 , HOH A:1427
BINDING SITE FOR RESIDUE BMA A 404
11
AC5
SOFTWARE
BMA A:404 , HOH A:1066 , HOH A:1339
BINDING SITE FOR RESIDUE MAN A 405
12
AC6
SOFTWARE
ASN B:257 , THR B:270 , FUC B:502 , NAG B:503 , HOH B:1106 , HOH B:1166 , HOH B:1502
BINDING SITE FOR RESIDUE NAG B 501
13
AC7
SOFTWARE
NAG B:501 , FUC D:502
BINDING SITE FOR RESIDUE FUC B 502
14
AC8
SOFTWARE
NAG B:501 , BMA B:504 , HOH B:1517
BINDING SITE FOR RESIDUE NAG B 503
15
AC9
SOFTWARE
NAG B:503
BINDING SITE FOR RESIDUE BMA B 504
16
BC1
SOFTWARE
ASN C:67 , THR C:69 , ASP C:100 , SER C:133 , FUC C:402 , NAG C:403 , HOH C:1366
BINDING SITE FOR RESIDUE NAG C 401
17
BC2
SOFTWARE
NAG C:401 , NAG C:403
BINDING SITE FOR RESIDUE FUC C 402
18
BC3
SOFTWARE
ILE C:132 , VAL C:134 , NAG C:401 , FUC C:402 , BMA C:404 , HOH C:1151
BINDING SITE FOR RESIDUE NAG C 403
19
BC4
SOFTWARE
GLN C:126 , NAG C:403 , MAN C:405 , MAN C:406 , HOH C:1081
BINDING SITE FOR RESIDUE BMA C 404
20
BC5
SOFTWARE
LEU C:141 , ASN C:142 , GLY C:144 , BMA C:404 , HOH C:1081 , HOH C:1093 , HOH C:1148 , HOH C:1188 , HOH C:1214 , HOH C:1365
BINDING SITE FOR RESIDUE MAN C 405
21
BC6
SOFTWARE
LYS C:147 , BMA C:404 , HOH C:1364
BINDING SITE FOR RESIDUE MAN C 406
22
BC7
SOFTWARE
ASN D:257 , FUC D:502 , NAG D:503 , HOH D:1332
BINDING SITE FOR RESIDUE NAG D 501
23
BC8
SOFTWARE
FUC B:502 , NAG D:501 , NAG D:503
BINDING SITE FOR RESIDUE FUC D 502
24
BC9
SOFTWARE
NAG D:501 , FUC D:502 , MAN D:504
BINDING SITE FOR RESIDUE NAG D 503
25
CC1
SOFTWARE
NAG D:503
BINDING SITE FOR RESIDUE MAN D 504
[
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: PEPTIDASE_A1 (A:14-238,C:14-238)
2: ASP_PROTEASE (A:29-40,C:29-40)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPTIDASE_A1
PS51767
Peptidase family A1 domain profile.
CARDA_CYNCA
85-501
2
A:14-238
C:14-238
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
CARDA_CYNCA
100-111
2
A:29-40
C:29-40
[
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_d1b5f_1 (A:,B:)
1b: SCOP_d1b5f_2 (C:,D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Acid proteases
(1120)
Superfamily
:
Acid proteases
(1120)
Family
:
Pepsin-like
(505)
Protein domain
:
Plant acid proteinase, phytepsin
(2)
Cynara cardunculus [TaxId: 4265]
(1)
1a
d1b5f.1
A:,B:
1b
d1b5f.2
C:,D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1b5fB00 (B:243-326)
1b: CATH_1b5fD00 (D:243-326)
1c: CATH_1b5fC00 (C:1-238)
1d: CATH_1b5fA00 (A:0-238)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Cathepsin D, subunit A; domain 1
(745)
Homologous Superfamily
:
Acid Proteases
(745)
Cynara cardunculus. Organism_taxid: 4265.
(1)
1a
1b5fB00
B:243-326
1b
1b5fD00
D:243-326
1c
1b5fC00
C:1-238
1d
1b5fA00
A:0-238
[
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
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 (127 KB)
Header - Asym.Unit
Biol.Unit 1 (120 KB)
Header - Biol.Unit 1
Biol.Unit 2 (62 KB)
Header - Biol.Unit 2
Biol.Unit 3 (62 KB)
Header - Biol.Unit 3
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
1B5F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
