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.
1XF1
Asym. Unit
Info
Asym.Unit (324 KB)
Biol.Unit 1 (314 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF C5A PEPTIDASE- A KEY VIRULENCE FACTOR FROM STREPTOCOCCUS
Authors
:
C. K. Brown, Z. Y. Gu, P. P. Cleary, Y. Matsuka, S. Olmstead, D. H. Ohlendorf, C. A. Earhart
Date
:
13 Sep 04 (Deposition) - 22 Nov 05 (Release) - 20 May 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
C5A Peptidase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. K. Brown, Z. Y. Gu, Y. V. Matsuka, S. S. Purushothaman, L. A. Winter, P. P. Cleary, S. B. Olmsted, D. H. Ohlendorf, C. A. Earhart
Structure Of The Streptococcal Cell Wall C5A Peptidase
Proc. Natl. Acad. Sci. Usa V. 102 18391 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 42)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: CITRIC ACID (CITa)
3b: CITRIC ACID (CITb)
3c: CITRIC ACID (CITc)
3d: CITRIC ACID (CITd)
3e: CITRIC ACID (CITe)
3f: CITRIC ACID (CITf)
4a: SELENOMETHIONINE (MSEa)
4aa: SELENOMETHIONINE (MSEaa)
4ab: SELENOMETHIONINE (MSEab)
4ac: SELENOMETHIONINE (MSEac)
4ad: SELENOMETHIONINE (MSEad)
4ae: SELENOMETHIONINE (MSEae)
4af: SELENOMETHIONINE (MSEaf)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
4y: SELENOMETHIONINE (MSEy)
4z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
CA
2
Ligand/Ion
CALCIUM ION
3
CIT
6
Ligand/Ion
CITRIC ACID
4
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:483 , HIS A:598 , ASN A:600 , ILE A:707 , PHE A:709
BINDING SITE FOR RESIDUE ACT A 1107
02
AC2
SOFTWARE
SER A:822 , ASN A:824 , ASP A:826 , ASN A:828 , ASP A:830 , HOH A:1264
BINDING SITE FOR RESIDUE CA A 1109
03
AC3
SOFTWARE
TYR A:268 , ASP A:312 , LEU A:479 , PHE A:713 , ASN A:841 , LYS A:868 , ILE A:912 , HOH A:1166 , HOH A:1182 , HOH A:1200 , HOH A:1641
BINDING SITE FOR RESIDUE CIT A 1101
04
AC4
SOFTWARE
ARG A:393 , GLY A:422 , PHE A:423 , LYS A:470 , SER A:472 , ARG A:473 , LEU A:497 , HOH A:1207 , HOH A:1520
BINDING SITE FOR RESIDUE CIT A 1103
05
AC5
SOFTWARE
ARG A:393 , ASP A:395 , ILE A:396 , ASP A:397 , PHE A:398 , HOH A:1158 , GLU B:983
BINDING SITE FOR RESIDUE CIT A 1105
06
AC6
SOFTWARE
GLY B:483 , HIS B:598 , ASN B:600 , ILE B:707 , PHE B:709
BINDING SITE FOR RESIDUE ACT B 1108
07
AC7
SOFTWARE
SER B:822 , ASN B:824 , ASP B:826 , ASN B:828 , ASP B:830 , HOH B:1390
BINDING SITE FOR RESIDUE CA B 1110
08
AC8
SOFTWARE
TYR B:268 , ASP B:312 , VAL B:316 , LEU B:479 , PHE B:713 , ASN B:841 , LYS B:868 , ILE B:912 , HOH B:1133 , HOH B:1136 , HOH B:1143 , HOH B:1200 , HOH B:1342 , HOH B:1346 , HOH B:1519
BINDING SITE FOR RESIDUE CIT B 1102
09
AC9
SOFTWARE
ARG B:393 , GLN B:419 , GLY B:422 , PHE B:423 , LYS B:470 , SER B:472 , ARG B:473 , LEU B:497 , HOH B:1336 , HOH B:1609
BINDING SITE FOR RESIDUE CIT B 1104
10
BC1
SOFTWARE
GLU A:983 , ARG B:393 , ASP B:395 , ILE B:396 , ASP B:397 , PHE B:398 , HOH B:1229
BINDING SITE FOR RESIDUE CIT B 1106
[
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
(3, 6)
Info
All PROSITE Patterns/Profiles
1: SUBTILASE_ASP (A:126-137,B:126-137)
2: SUBTILASE_HIS (A:193-203,B:193-203)
3: SUBTILASE_SER (A:510-520,B:510-520)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUBTILASE_ASP
PS00136
Serine proteases, subtilase family, aspartic acid active site.
C5AP_STRPY
126-137
2
A:126-137
B:126-137
2
SUBTILASE_HIS
PS00137
Serine proteases, subtilase family, histidine active site.
C5AP_STRPY
193-203
2
A:193-203
B:193-203
3
SUBTILASE_SER
PS00138
Serine proteases, subtilase family, serine active site.
C5AP_STRPY
510-520
2
A:510-520
B:510-520
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(4, 8)
Info
all PFAM domains
1a: PFAM_CHU_C_1xf1B01 (B:816-926)
1b: PFAM_CHU_C_1xf1B02 (B:816-926)
2a: PFAM_DUF1034_1xf1B03 (B:597-707)
2b: PFAM_DUF1034_1xf1B04 (B:597-707)
3a: PFAM_PA_1xf1B05 (B:365-449)
3b: PFAM_PA_1xf1B06 (B:365-449)
4a: PFAM_Peptidase_S8_1xf1B07 (B:125-582)
4b: PFAM_Peptidase_S8_1xf1B08 (B:125-582)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
E-set
(290)
Family
:
CHU_C
(1)
Streptococcus pyogenes
(1)
1a
CHU_C-1xf1B01
B:816-926
1b
CHU_C-1xf1B02
B:816-926
Family
:
DUF1034
(1)
Streptococcus pyogenes
(1)
2a
DUF1034-1xf1B03
B:597-707
2b
DUF1034-1xf1B04
B:597-707
Clan
:
no clan defined [family: PA]
(15)
Family
:
PA
(15)
Streptococcus pyogenes
(1)
3a
PA-1xf1B05
B:365-449
3b
PA-1xf1B06
B:365-449
Clan
:
no clan defined [family: Peptidase_S8]
(104)
Family
:
Peptidase_S8
(104)
Streptococcus pyogenes
(1)
4a
Peptidase_S8-1xf1B07
B:125-582
4b
Peptidase_S8-1xf1B08
B:125-582
[
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 (324 KB)
Header - Asym.Unit
Biol.Unit 1 (314 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
1XF1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help