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.
2X4M
Asym. Unit
Info
Asym.Unit (200 KB)
Biol.Unit 1 (52 KB)
Biol.Unit 2 (50 KB)
Biol.Unit 3 (51 KB)
Biol.Unit 4 (51 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
YERSINIA PESTIS PLASMINOGEN ACTIVATOR PLA
Authors
:
E. Eren, M. Murphy, J. Goguen, B. Van Den Berg
Date
:
05 Feb 10 (Deposition) - 28 Jul 10 (Release) - 28 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Omptin, Transmembrane, Aspartyl Protease, Cell Outer Membrane, Protease, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Eren, M. Murphy, J. Goguen, B. Van Den Berg
An Active Site Water Network In The Plasminogen Activator Pla From Yersinia Pestis
Structure V. 18 809 2010
[
close entry info
]
Hetero Components
(2, 37)
Info
All Hetero Components
1a: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ea)
1b: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eb)
1c: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ec)
1d: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ed)
1e: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ee)
1f: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ef)
1g: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eg)
1h: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eh)
1i: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ei)
1j: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ej)
1k: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ek)
1l: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8El)
1m: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Em)
1n: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8En)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C8E
14
Ligand/Ion
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2
SO4
23
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(37, 37)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:236 , ASN A:238 , TYR A:290
BINDING SITE FOR RESIDUE SO4 A1295
02
AC2
SOFTWARE
ARG A:171 , HIS A:203 , ASN A:205 , ARG A:216 , HOH A:2032
BINDING SITE FOR RESIDUE SO4 A1296
03
AC3
SOFTWARE
LYS A:54 , ARG A:70 , GLU A:111 , ASP A:113 , GLN A:135 , LYS A:195
BINDING SITE FOR RESIDUE SO4 A1297
04
AC4
SOFTWARE
ALA A:103 , GLY A:145 , GLY A:146 , LYS A:161 , HOH A:2012
BINDING SITE FOR RESIDUE SO4 A1298
05
AC5
SOFTWARE
ASP A:84 , TYR A:150 , HIS A:208 , ARG A:211 , C8E A:1304 , HOH A:2033
BINDING SITE FOR RESIDUE SO4 A1299
06
AC6
SOFTWARE
ILE A:57 , ARG A:70 , TYR A:112
BINDING SITE FOR RESIDUE C8E A1300
07
AC7
SOFTWARE
LEU A:53 , TRP A:72 , ASN A:110 , ARG A:138
BINDING SITE FOR RESIDUE C8E A1301
08
AC8
SOFTWARE
TYR A:126 , LYS A:127 , GLY A:181 , GLN A:182 , LEU C:121 , ASP C:123
BINDING SITE FOR RESIDUE C8E A1302
09
AC9
SOFTWARE
PRO A:175 , TYR A:176 , ILE A:177 , TRP A:199
BINDING SITE FOR RESIDUE C8E A1303
10
BC1
SOFTWARE
MET A:30 , HIS A:208 , GLU A:217 , SO4 A:1299
BINDING SITE FOR RESIDUE C8E A1304
11
BC2
SOFTWARE
SER A:3 , ALA B:103 , GLY B:146 , LYS B:161 , HOH B:2013
BINDING SITE FOR RESIDUE SO4 B1299
12
BC3
SOFTWARE
LYS B:249 , ASP B:251 , GLU B:252
BINDING SITE FOR RESIDUE SO4 B1300
13
BC4
SOFTWARE
ARG B:171 , HIS B:203 , ASN B:205 , ARG B:216
BINDING SITE FOR RESIDUE SO4 B1301
14
BC5
SOFTWARE
ASP B:97 , SO4 B:1303
BINDING SITE FOR RESIDUE SO4 B1302
15
BC6
SOFTWARE
ASP B:84 , HIS B:208 , ARG B:211 , SO4 B:1302 , C8E B:1304
BINDING SITE FOR RESIDUE SO4 B1303
16
BC7
SOFTWARE
GLU B:29 , MET B:30 , GLU B:217 , ALA B:275 , SO4 B:1303
BINDING SITE FOR RESIDUE C8E B1304
17
BC8
SOFTWARE
LEU B:53 , GLY B:71 , TRP B:72 , ASN B:110 , GLU B:111
BINDING SITE FOR RESIDUE C8E B1305
18
BC9
SOFTWARE
LEU B:179 , ALA B:180 , GLY B:181 , ALA B:192 , LEU B:193 , PHE B:194 , THR B:227
BINDING SITE FOR RESIDUE C8E B1306
19
CC1
SOFTWARE
LYS C:54 , ARG C:70 , GLU C:111 , ASP C:113 , GLN C:135 , LYS C:195 , VAL C:228 , THR C:246
BINDING SITE FOR RESIDUE SO4 C1294
20
CC2
SOFTWARE
GLN B:92 , SER B:93 , GLU B:94 , ASN C:125 , TYR C:126 , TYR C:183 , ILE C:185
BINDING SITE FOR RESIDUE SO4 C1295
21
CC3
SOFTWARE
ASP C:84 , HIS C:208 , ARG C:211
BINDING SITE FOR RESIDUE SO4 C1296
22
CC4
SOFTWARE
ARG C:171 , HIS C:203 , ASN C:205 , ARG C:216
BINDING SITE FOR RESIDUE SO4 C1297
23
CC5
SOFTWARE
GLY A:162 , VAL A:163 , ARG A:164 , VAL C:163 , ARG C:164
BINDING SITE FOR RESIDUE SO4 C1298
24
CC6
SOFTWARE
ALA C:103 , GLY C:145 , GLY C:146 , LYS C:161 , SER D:3
BINDING SITE FOR RESIDUE SO4 C1299
25
CC7
SOFTWARE
MET C:30 , HIS C:208 , GLU C:217
BINDING SITE FOR RESIDUE C8E C1300
26
CC8
SOFTWARE
LEU C:53 , GLY C:71 , ASN C:110
BINDING SITE FOR RESIDUE C8E C1301
27
CC9
SOFTWARE
ALA C:69 , TYR C:112
BINDING SITE FOR RESIDUE C8E C1302
28
DC1
SOFTWARE
LYS D:54 , ARG D:70 , GLU D:111 , ASP D:113 , LYS D:195 , VAL D:228 , THR D:246 , HOH D:2026
BINDING SITE FOR RESIDUE SO4 D1295
29
DC2
SOFTWARE
GLY D:145 , GLY D:146 , LYS D:161 , HOH D:2009 , HOH D:2012
BINDING SITE FOR RESIDUE SO4 D1296
30
DC3
SOFTWARE
ARG D:171 , SER D:173 , ARG D:201 , HIS D:203
BINDING SITE FOR RESIDUE SO4 D1297
31
DC4
SOFTWARE
ARG D:171 , HIS D:203 , ASN D:205
BINDING SITE FOR RESIDUE SO4 D1298
32
DC5
SOFTWARE
THR D:236 , TYR D:290 , HOH D:2027
BINDING SITE FOR RESIDUE SO4 D1299
33
DC6
SOFTWARE
VAL B:163 , ARG B:164 , ARG D:164
BINDING SITE FOR RESIDUE SO4 D1300
34
DC7
SOFTWARE
ASP D:84 , HIS D:208 , ARG D:211 , C8E D:1304 , HOH D:2007
BINDING SITE FOR RESIDUE SO4 D1301
35
DC8
SOFTWARE
LYS D:54 , GLY D:55 , TRP D:72 , ASN D:110 , GLU D:111
BINDING SITE FOR RESIDUE C8E D1302
36
DC9
SOFTWARE
GLY D:55 , ASP D:56 , ALA D:69 , ARG D:70 , TYR D:112
BINDING SITE FOR RESIDUE C8E D1303
37
EC1
SOFTWARE
GLU D:29 , HIS D:208 , ARG D:211 , SO4 D:1301
BINDING SITE FOR RESIDUE C8E D1304
[
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, 8)
Info
All PROSITE Patterns/Profiles
1: OMPTIN_1 (A:95-104,B:95-104,C:95-104,D:95-10...)
2: OMPTIN_2 (A:132-148,B:132-148,C:132-148,D:13...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
OMPTIN_1
PS00834
Aspartyl proteases, omptin family signature 1.
COLY_YERPE
115-124
4
A:95-104
B:95-104
C:95-104
D:95-104
2
OMPTIN_2
PS00835
Aspartyl proteases, omptin family signature 2.
COLY_YERPE
152-168
4
A:132-148
B:132-148
C:132-148
D:132-148
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d2x4ma_ (A:)
1b: SCOP_d2x4mb_ (B:)
1c: SCOP_d2x4mc_ (C:)
1d: SCOP_d2x4md_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Transmembrane beta-barrels
(143)
Superfamily
:
OMPT-like
(6)
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Yersinia pestis [TaxId: 632]
(3)
1a
d2x4ma_
A:
1b
d2x4mb_
B:
1c
d2x4mc_
C:
1d
d2x4md_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2x4mB00 (B:13-298)
1b: CATH_2x4mC00 (C:3-293)
1c: CATH_2x4mA00 (A:2-294)
1d: CATH_2x4mD00 (D:2-294)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Lipocalin
(526)
Homologous Superfamily
:
OMPT-like
(4)
Yersinia pestis. Organism_taxid: 632.
(3)
1a
2x4mB00
B:13-298
1b
2x4mC00
C:3-293
1c
2x4mA00
A:2-294
1d
2x4mD00
D:2-294
[
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 (200 KB)
Header - Asym.Unit
Biol.Unit 1 (52 KB)
Header - Biol.Unit 1
Biol.Unit 2 (50 KB)
Header - Biol.Unit 2
Biol.Unit 3 (51 KB)
Header - Biol.Unit 3
Biol.Unit 4 (51 KB)
Header - Biol.Unit 4
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
2X4M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
