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.
3BJW
Asym. Unit
Info
Asym.Unit (197 KB)
Biol.Unit 1 (185 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 ECARPHOLIN S COMPLEXED WITH SURAMIN
Authors
:
X. Zhou, J. Sivaraman
Date
:
04 Dec 07 (Deposition) - 18 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Snake Venom, Phospholipase A2, Suramin, Ser49, Complex, Calcium, Hydrolase, Lipid Degradation, Metal-Binding, Secreted, Toxin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Zhou, T. C. Tan, S. Valiyaveettil, M. L. Go, R. M. Kini, A. Velazquez-Campoy, J. Sivaraman
Structural Characterization Of Myotoxic Ecarpholin S From Echis Carinatus Venom
Biophys. J. V. 95 3366 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 12)
Info
All Hetero Components
1a: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRa)
1b: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRb)
1c: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRc)
1d: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRd)
1e: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRe)
1f: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRf)
1g: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRg)
1h: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRh)
1i: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRi)
1j: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRj)
1k: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRk)
1l: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYL... (SVRl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SVR
12
Ligand/Ion
8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC ACID
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:36 , PHE A:124 , TRP A:125 , LYS A:127 , GLY A:128 , HOH A:522 , HOH A:527 , HOH A:536 , VAL E:3 , GLN E:11 , ARG E:77 , SVR E:503 , SVR E:510 , VAL G:2 , VAL G:3 , GLY G:6 , ARG G:72 , HOH G:511 , PHE H:124
BINDING SITE FOR RESIDUE SVR A 508
02
AC2
SOFTWARE
SER A:17 , PRO A:18 , PHE A:19 , PRO A:20 , VAL B:2 , VAL B:3 , LEU B:5 , GLY B:6 , ILE B:10 , LYS B:16 , SER B:17 , PRO B:18 , PHE B:19 , PRO B:20 , SER B:21 , THR B:23 , LYS B:115 , SVR B:512 , HOH B:522 , HOH B:541 , HOH B:556 , HOH B:563 , LYS F:116 , ASN F:122 , PHE F:124 , LYS G:116 , SVR G:506 , HOH G:515
BINDING SITE FOR RESIDUE SVR B 501
03
AC3
SOFTWARE
VAL A:2 , VAL A:3 , THR A:70 , ARG A:72 , VAL B:3 , LYS B:7 , ILE B:10 , GLN B:11 , GLU B:12 , THR B:13 , GLY B:14 , ARG B:107 , LEU B:110 , SVR B:501 , HOH B:517 , HOH B:518 , HOH B:539 , HOH B:547 , LYS G:16 , TYR G:113 , ASN G:114 , LYS G:115 , LYS G:116 , TYR G:117 , TRP G:125 , SVR G:506 , HOH G:538 , HOH G:541
BINDING SITE FOR RESIDUE SVR B 512
04
AC4
SOFTWARE
PRO C:36 , PHE C:124 , TRP C:125 , LYS C:127 , GLY C:128 , HOH C:522 , HOH C:551 , VAL D:2 , VAL D:3 , GLY D:6 , LYS D:7 , LYS D:69 , ARG D:72 , HOH D:146 , HOH D:161 , PHE E:124 , VAL H:2 , VAL H:3 , GLN H:11 , PHE H:19 , ARG H:77 , SVR H:504 , SVR H:511
BINDING SITE FOR RESIDUE SVR C 505
05
AC5
SOFTWARE
PHE B:124 , VAL C:2 , VAL C:3 , GLY C:6 , PRO C:18 , LYS C:69 , ARG C:72 , HOH C:508 , HOH C:515 , HOH C:524 , HOH C:527 , HOH C:549 , PRO D:36 , PHE D:124 , LYS D:127 , VAL F:3 , GLN F:11 , ARG F:77 , SVR F:502 , SVR F:509 , HOH F:519
BINDING SITE FOR RESIDUE SVR C 507
06
AC6
SOFTWARE
LYS A:116 , SVR A:508 , VAL E:2 , VAL E:3 , LEU E:5 , GLY E:6 , ILE E:10 , LYS E:16 , SER E:17 , PRO E:18 , PHE E:19 , PRO E:20 , SER E:21 , THR E:23 , LYS E:115 , SVR E:510 , HOH E:513 , HOH E:530 , HOH E:537 , SER G:17 , PRO G:18 , PHE G:19 , PRO G:20 , LYS H:116 , ASN H:122 , PHE H:124
BINDING SITE FOR RESIDUE SVR E 503
07
AC7
SOFTWARE
LYS A:16 , TYR A:113 , ASN A:114 , LYS A:115 , TYR A:117 , TRP A:125 , SVR A:508 , HOH A:524 , HOH A:530 , VAL E:3 , LYS E:7 , ILE E:10 , GLN E:11 , GLU E:12 , THR E:13 , GLY E:14 , ARG E:107 , LEU E:110 , ASN E:111 , SVR E:503 , HOH E:541 , VAL G:2 , VAL G:3 , THR G:70 , ARG G:72
BINDING SITE FOR RESIDUE SVR E 510
08
AC8
SOFTWARE
LYS B:116 , ASN B:122 , PHE B:124 , SER C:17 , PHE C:19 , PRO C:20 , SVR C:507 , LYS D:116 , HOH D:140 , VAL F:2 , LEU F:5 , GLY F:6 , ILE F:10 , LYS F:16 , SER F:17 , PRO F:18 , PRO F:20 , SER F:21 , THR F:23 , LYS F:115 , SVR F:509 , HOH F:512 , HOH F:527 , HOH F:554
BINDING SITE FOR RESIDUE SVR F 502
09
AC9
SOFTWARE
VAL C:2 , VAL C:3 , THR C:23 , THR C:70 , SVR C:507 , LYS D:16 , TYR D:113 , ASN D:114 , LYS D:115 , PRO D:121 , PHE D:124 , TRP D:125 , VAL F:3 , LYS F:7 , ILE F:10 , GLN F:11 , GLU F:12 , THR F:13 , GLY F:14 , ARG F:107 , LEU F:110 , SVR F:502 , HOH F:520 , HOH F:551
BINDING SITE FOR RESIDUE SVR F 509
10
BC1
SOFTWARE
VAL A:2 , VAL A:3 , GLY A:6 , LYS A:7 , ARG A:72 , LYS A:74 , HOH A:509 , VAL B:2 , VAL B:3 , GLN B:11 , ARG B:77 , SVR B:501 , SVR B:512 , HOH B:518 , PHE F:124 , TRP F:125 , HOH F:507 , PRO G:36 , PHE G:124 , TRP G:125 , LYS G:127 , GLY G:128 , HOH G:521 , HOH G:522 , HOH G:528 , HOH G:531 , HOH G:536 , HOH G:540 , HOH G:541
BINDING SITE FOR RESIDUE SVR G 506
11
BC2
SOFTWARE
LYS C:116 , SVR C:505 , HOH C:512 , SER D:17 , PRO D:18 , PHE D:19 , PRO D:20 , PRO E:121 , ASN E:122 , PHE E:124 , VAL H:2 , LEU H:5 , GLY H:6 , ILE H:10 , LYS H:16 , SER H:17 , PRO H:18 , PHE H:19 , PRO H:20 , SER H:21 , THR H:23 , LYS H:115 , SVR H:511 , HOH H:518 , HOH H:530
BINDING SITE FOR RESIDUE SVR H 504
12
BC3
SOFTWARE
LYS C:16 , TYR C:113 , ASN C:114 , LYS C:115 , LYS C:116 , TYR C:117 , TRP C:125 , SVR C:505 , VAL D:2 , VAL D:3 , THR D:70 , ARG D:72 , HOH D:151 , LYS H:7 , ILE H:10 , GLN H:11 , GLU H:12 , THR H:13 , GLY H:14 , ARG H:107 , LEU H:110 , SVR H:504 , HOH H:525 , HOH H:537
BINDING SITE FOR RESIDUE SVR H 511
[
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, 16)
Info
All PROSITE Patterns/Profiles
1: PA2_HIS (A:44-51,B:44-51,C:44-51,D:44-51,E:...)
2: PA2_ASP (A:95-105,B:95-105,C:95-105,D:95-10...)
;
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.
PA2HS_ECHCA
43-50
8
A:44-51
B:44-51
C:44-51
D:44-51
E:44-51
F:44-51
G:44-51
H:44-51
2
PA2_ASP
PS00119
Phospholipase A2 aspartic acid active site.
PA2HS_ECHCA
85-95
8
A:95-105
B:95-105
C:95-105
D:95-105
E:95-105
F:95-105
G:95-105
H:95-105
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d3bjwa_ (A:)
1b: SCOP_d3bjwh_ (H:)
1c: SCOP_d3bjwb_ (B:)
1d: SCOP_d3bjwc_ (C:)
1e: SCOP_d3bjwd_ (D:)
1f: SCOP_d3bjwe_ (E:)
1g: SCOP_d3bjwf_ (F:)
1h: SCOP_d3bjwg_ (G:)
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
:
automated matches
(75)
Saw-scaled viper (Echis carinatus) [TaxId: 40353]
(3)
1a
d3bjwa_
A:
1b
d3bjwh_
H:
1c
d3bjwb_
B:
1d
d3bjwc_
C:
1e
d3bjwd_
D:
1f
d3bjwe_
E:
1g
d3bjwf_
F:
1h
d3bjwg_
G:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_3bjwA00 (A:1-133)
1b: CATH_3bjwH00 (H:1-133)
1c: CATH_3bjwB00 (B:1-133)
1d: CATH_3bjwC00 (C:1-133)
1e: CATH_3bjwD00 (D:1-133)
1f: CATH_3bjwE00 (E:1-133)
1g: CATH_3bjwF00 (F:1-133)
1h: CATH_3bjwG00 (G:1-133)
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)
Saw-scaled viper (Echis carinatus)
(4)
1a
3bjwA00
A:1-133
1b
3bjwH00
H:1-133
1c
3bjwB00
B:1-133
1d
3bjwC00
C:1-133
1e
3bjwD00
D:1-133
1f
3bjwE00
E:1-133
1g
3bjwF00
F:1-133
1h
3bjwG00
G:1-133
[
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
Chain E
Chain F
Chain G
Chain H
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 (197 KB)
Header - Asym.Unit
Biol.Unit 1 (185 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
3BJW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help