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2X4M
Biol. Unit 3
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)
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(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, 9)
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
3
Ligand/Ion
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(10, 10)
Info
All Sites
01: AC8 (SOFTWARE)
02: CC1 (SOFTWARE)
03: CC2 (SOFTWARE)
04: CC3 (SOFTWARE)
05: CC4 (SOFTWARE)
06: CC5 (SOFTWARE)
07: CC6 (SOFTWARE)
08: CC7 (SOFTWARE)
09: CC8 (SOFTWARE)
10: CC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
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
04
CC3
SOFTWARE
ASP C:84 , HIS C:208 , ARG C:211
BINDING SITE FOR RESIDUE SO4 C1296
05
CC4
SOFTWARE
ARG C:171 , HIS C:203 , ASN C:205 , ARG C:216
BINDING SITE FOR RESIDUE SO4 C1297
06
CC5
SOFTWARE
GLY A:162 , VAL A:163 , ARG A:164 , VAL C:163 , ARG C:164
BINDING SITE FOR RESIDUE SO4 C1298
07
CC6
SOFTWARE
ALA C:103 , GLY C:145 , GLY C:146 , LYS C:161 , SER D:3
BINDING SITE FOR RESIDUE SO4 C1299
08
CC7
SOFTWARE
MET C:30 , HIS C:208 , GLU C:217
BINDING SITE FOR RESIDUE C8E C1300
09
CC8
SOFTWARE
LEU C:53 , GLY C:71 , ASN C:110
BINDING SITE FOR RESIDUE C8E C1301
10
CC9
SOFTWARE
ALA C:69 , TYR C:112
BINDING SITE FOR RESIDUE C8E C1302
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: OMPTIN_1 (C:95-104)
2: OMPTIN_2 (C:132-148)
;
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
1
-
-
C:95-104
-
2
OMPTIN_2
PS00835
Aspartyl proteases, omptin family signature 2.
COLY_YERPE
152-168
1
-
-
C:132-148
-
[
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]
Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2x4ma_ (A:)
1b: SCOP_d2x4mb_ (B:)
1c: SCOP_d2x4mc_ (C:)
1d: SCOP_d2x4md_ (D:)
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)
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
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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)
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)
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(
)
(
)
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
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
(currently selected atoms:
all
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Protein
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain C
Asymmetric Unit 1
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Example Commands
Example Command
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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)
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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
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