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.
3WOO
Asym. Unit
Info
Asym.Unit (246 KB)
Biol.Unit 1 (239 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 THE DAP BII HEXAPEPTIDE COMPLEX I
Authors
:
Y. Sakamoto, Y. Suzuki, I. Iizuka, C. Tateoka, S. Roppongi, M. Fujimoto T. Nonaka, W. Ogasawara, N. Tanaka
Date
:
29 Dec 13 (Deposition) - 03 Sep 14 (Release) - 03 Sep 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Chymotrypsin Fold, S46 Peptidase, Hydrolase-Hormone Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Sakamoto, Y. Suzuki, I. Iizuka, C. Tateoka, S. Roppongi, M. Fujimoto, K. Inaka, H. Tanaka, M. Masaki, K. Ohta, H. Okada, T. Nonaka, Y. Morikawa, K. T. Nakamura, W. Ogasawara, N. Tanaka
S46 Peptidases Are The First Exopeptidases To Be Members Of Clan Pa
Sci Rep V. 4 4977 2014
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
12
Ligand/Ion
GLYCEROL
2
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:598 , PHE A:600 , ILE A:639 , HOH A:919 , HOH A:1053 , HOH A:1125 , HOH A:1410 , ASP B:593 , GLY B:594 , HOH B:965
BINDING SITE FOR RESIDUE GOL A 801
02
AC2
SOFTWARE
ASP A:59 , LYS A:251 , HIS A:252 , TRP A:253 , LYS A:255 , HOH A:1219
BINDING SITE FOR RESIDUE GOL A 802
03
AC3
SOFTWARE
GLY A:68 , ARG A:175 , HOH A:952 , HOH A:1208 , HOH A:1283 , HOH A:1357
BINDING SITE FOR RESIDUE GOL A 803
04
AC4
SOFTWARE
TYR A:89 , LYS A:208 , ASP A:212 , ALA A:322 , ALA A:326 , ASN A:329 , HOH A:1439
BINDING SITE FOR RESIDUE GOL A 804
05
AC5
SOFTWARE
CYS A:87 , ALA A:88 , GLY A:90 , ALA A:91 , TYR A:228 , HOH A:944 , HOH A:1026 , HOH A:1032 , HOH A:1157
BINDING SITE FOR RESIDUE GOL A 805
06
AC6
SOFTWARE
ARG A:413 , LEU A:535 , GLU A:539 , ARG A:542 , HOH A:1099 , HOH A:1195 , HOH A:1396
BINDING SITE FOR RESIDUE GOL A 806
07
AC7
SOFTWARE
ASN A:101 , GLN A:318
BINDING SITE FOR RESIDUE GOL A 807
08
AC8
SOFTWARE
ALA A:257 , ASP A:258 , ARG A:699 , HOH A:920 , HOH A:1311
BINDING SITE FOR RESIDUE GOL A 808
09
AC9
SOFTWARE
LYS A:47 , GLU A:635 , HIS A:665 , HOH A:1436
BINDING SITE FOR RESIDUE ZN A 809
10
BC1
SOFTWARE
GLU A:505 , LYS A:508 , HOH A:1433 , GLU B:438
BINDING SITE FOR RESIDUE ZN A 810
11
BC2
SOFTWARE
ASP A:593 , GLY A:594 , HOH A:945 , THR B:598 , PHE B:600 , ILE B:639 , HOH B:942 , HOH B:1131
BINDING SITE FOR RESIDUE GOL B 801
12
BC3
SOFTWARE
LEU B:127 , ASP B:128 , PHE B:172 , LEU B:191 , LYS B:251
BINDING SITE FOR RESIDUE GOL B 802
13
BC4
SOFTWARE
ASP B:59 , LYS B:251 , HIS B:252 , TRP B:253 , LYS B:255 , PRO B:468
BINDING SITE FOR RESIDUE GOL B 803
14
BC5
SOFTWARE
GLY B:68 , ARG B:175 , ASN B:190 , HOH B:955
BINDING SITE FOR RESIDUE GOL B 804
15
BC6
SOFTWARE
LYS B:47 , GLU B:635 , HIS B:665 , HOH B:1295
BINDING SITE FOR RESIDUE ZN B 805
16
BC7
SOFTWARE
GLU A:438 , GLU B:505 , LYS B:508 , HOH B:1294
BINDING SITE FOR RESIDUE ZN B 806
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(1, 2)
Info
All Exons
Exon 1.2a (C:1-5 | D:1-5)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2a
2: Boundary 1.2a/1.3
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
1.1
ENST00000366667
1
ENSE00001442280
chr1:
230850043-230849832
212
ANGT_HUMAN
-
0
0
-
-
1.2a
ENST00000366667
2a
ENSE00001442279
chr1:
230846599-230845741
859
ANGT_HUMAN
1-286
286
2
C:1-5
D:1-5
5
5
1.3
ENST00000366667
3
ENSE00000921429
chr1:
230841946-230841679
268
ANGT_HUMAN
286-375
90
0
-
-
1.4
ENST00000366667
4
ENSE00000921430
chr1:
230840083-230839939
145
ANGT_HUMAN
375-423
49
0
-
-
1.5b
ENST00000366667
5b
ENSE00001920401
chr1:
230839075-230838269
807
ANGT_HUMAN
424-485
62
0
-
-
[
close EXON info
]
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
(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 (246 KB)
Header - Asym.Unit
Biol.Unit 1 (239 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
3WOO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help