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.
1J1A
Asym. Unit
Info
Asym.Unit (49 KB)
Biol.Unit 1 (44 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PANCREATIC SECRETORY PHOSPHOLIPASE A2 (IIA) WITH ANTI-INFLAMMATORY ACTIVITY
Authors
:
K. A. Hansford, R. C. Reid, C. I. Clark, J. D. A. Tyndall, M. W. Whitehouse, T. Guthrie, R. P. Mcgeary, K. Schafer, J. L. Martin, D. P. Fairlie
Date
:
03 Dec 02 (Deposition) - 18 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Medicinal Chemistry, Enzyme Inhibitor, Structure-Activity Relationships, Inflammation, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. A. Hansford, R. C. Reid, C. I. Clark, J. D. A. Tyndall, M. W. Whitehouse, T. Guthrie, R. P. Mcgeary, K. Schafer, J. L. Martin, D. P. Fairlie
D-Tyrosine As A Chiral Precusor To Potent Inhibitors Of Human Nonpancreatic Secretory Phospholipase A2 (Iia) With Antiinflammatory Activity
Chembiochem V. 4 181 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: (S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PH... (BHPa)
1b: (S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PH... (BHPb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BHP
2
Ligand/Ion
(S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PHENYL-HEPTANOYLAMINO)-PENTANOIC ACID
2
CA
4
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:27 , GLY A:29 , GLY A:31 , ASP A:48 , BHP A:1301
BINDING SITE FOR RESIDUE CA A 201
2
AC2
SOFTWARE
PHE A:23 , GLY A:25 , TYR A:112 , ASN A:114 , HOH A:309 , HOH A:325
BINDING SITE FOR RESIDUE CA A 202
3
AC3
SOFTWARE
HIS B:27 , GLY B:29 , GLY B:31 , ASP B:48 , BHP B:2301
BINDING SITE FOR RESIDUE CA B 201
4
AC4
SOFTWARE
PHE B:23 , GLY B:25 , TYR B:112 , ASN B:114 , HOH B:376 , HOH B:392
BINDING SITE FOR RESIDUE CA B 202
5
AC5
SOFTWARE
LEU A:2 , PHE A:5 , HIS A:6 , ALA A:17 , GLY A:22 , PHE A:23 , HIS A:27 , GLY A:29 , VAL A:30 , GLY A:31 , CYS A:44 , HIS A:47 , ASP A:48 , TYR A:51 , LYS A:62 , CA A:201 , HOH A:332 , HOH A:361 , PHE B:23 , VAL B:30 , BHP B:2301
BINDING SITE FOR RESIDUE BHP A 1301
6
AC6
SOFTWARE
ALA A:18 , PHE A:23 , VAL A:30 , BHP A:1301 , PHE B:5 , ALA B:17 , GLY B:22 , PHE B:23 , HIS B:27 , CYS B:28 , GLY B:29 , VAL B:30 , GLY B:31 , CYS B:44 , HIS B:47 , ASP B:48 , TYR B:51 , LYS B:62 , CA B:201 , HOH B:399 , HOH B:415 , HOH B:428
BINDING SITE FOR RESIDUE BHP B 2301
[
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: PA2_HIS (A:43-50,B:43-50)
2: PA2_ASP (A:87-97,B:87-97)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PA2_HIS
PS00118
Phospholipase A2 histidine active site.
PA2GA_HUMAN
63-70
2
A:43-50
B:43-50
2
PA2_ASP
PS00119
Phospholipase A2 aspartic acid active site.
PA2GA_HUMAN
107-117
2
A:87-97
B:87-97
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.3e (A:1-42 | B:1-42)
Exon 1.3g (A:42-78 | B:42-78)
Exon 1.4d (A:78-124 | B:78-124)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3c/1.3e
2: Boundary 1.3e/1.3g
3: Boundary 1.3g/1.4d
4: Boundary 1.4d/-
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
1.2c
ENST00000400520
2c
ENSE00001543334
chr1:
20306111-20306073
39
PA2GA_HUMAN
-
0
0
-
-
1.3c
ENST00000400520
3c
ENSE00002182826
chr1:
20305372-20305227
146
PA2GA_HUMAN
1-14
14
0
-
-
1.3e
ENST00000400520
3e
ENSE00001326822
chr1:
20305017-20304873
145
PA2GA_HUMAN
14-62
49
2
A:1-42
B:1-42
42
42
1.3g
ENST00000400520
3g
ENSE00000873019
chr1:
20304614-20304508
107
PA2GA_HUMAN
62-98
37
2
A:42-78
B:42-78
37
37
1.4d
ENST00000400520
4d
ENSE00001543318
chr1:
20302336-20301929
408
PA2GA_HUMAN
98-144
47
2
A:78-124
B:78-124
47
47
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1j1aa_ (A:)
1b: SCOP_d1j1ab_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Phospholipase A2, PLA2
(282)
Superfamily
:
Phospholipase A2, PLA2
(282)
Family
:
Vertebrate phospholipase A2
(271)
Protein domain
:
Phospholipase A2
(72)
Human (Homo sapiens), synovial fluid [TaxId: 9606]
(16)
1a
d1j1aa_
A:
1b
d1j1ab_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1j1aA00 (A:1-124)
1b: CATH_1j1aB00 (B:1-124)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Phospholipase A2
(241)
Homologous Superfamily
:
Phospholipase A2
(241)
Human (Homo sapiens)
(15)
1a
1j1aA00
A:1-124
1b
1j1aB00
B:1-124
[
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
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 (49 KB)
Header - Asym.Unit
Biol.Unit 1 (44 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
1J1A
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
