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.
3WNO
Asym. Unit
Info
Asym.Unit (270 KB)
Biol.Unit 1 (133 KB)
Biol.Unit 2 (135 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
D308A MUTANT OF BACILLUS CIRCULANS T-3040 CYCLOISOMALTOOLIGOSACCHARIDE GLUCANOTRANSFERASE COMPLEXED WITH CYCLOISOMALTOOCTAOSE
Authors
:
N. Suzuki, Z. Fujimoto, Y. M. Kim, M. Momma, N. Kishine, R. Suzuki, M. Kob A. Kimura, K. Funane
Date
:
10 Dec 13 (Deposition) - 05 Feb 14 (Release) - 04 Mar 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
C2 Type Immunoglobulin Fold, (Beta/Alpha)8-Barrel, Beta-Jelly Roll, Greek Key, Glycoside Hydrolase, Alpha-1, 6-Glucan, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Suzuki, Z. Fujimoto, Y. M. Kim, M. Momma, N. Kishine, R. Suzuki, S. Suzuki, S. Kitamura, M. Kobayashi, A. Kimura, K. Funane
Structural Elucidation Of The Cyclization Mechanism Of Alpha-1, 6-Glucan By Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase.
J. Biol. Chem. V. 289 12040 2014
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 64)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
3a: ALPHA-D-GLUCOSE (GLCa)
3aa: ALPHA-D-GLUCOSE (GLCaa)
3ab: ALPHA-D-GLUCOSE (GLCab)
3ac: ALPHA-D-GLUCOSE (GLCac)
3ad: ALPHA-D-GLUCOSE (GLCad)
3ae: ALPHA-D-GLUCOSE (GLCae)
3af: ALPHA-D-GLUCOSE (GLCaf)
3ag: ALPHA-D-GLUCOSE (GLCag)
3ah: ALPHA-D-GLUCOSE (GLCah)
3ai: ALPHA-D-GLUCOSE (GLCai)
3aj: ALPHA-D-GLUCOSE (GLCaj)
3b: ALPHA-D-GLUCOSE (GLCb)
3c: ALPHA-D-GLUCOSE (GLCc)
3d: ALPHA-D-GLUCOSE (GLCd)
3e: ALPHA-D-GLUCOSE (GLCe)
3f: ALPHA-D-GLUCOSE (GLCf)
3g: ALPHA-D-GLUCOSE (GLCg)
3h: ALPHA-D-GLUCOSE (GLCh)
3i: ALPHA-D-GLUCOSE (GLCi)
3j: ALPHA-D-GLUCOSE (GLCj)
3k: ALPHA-D-GLUCOSE (GLCk)
3l: ALPHA-D-GLUCOSE (GLCl)
3m: ALPHA-D-GLUCOSE (GLCm)
3n: ALPHA-D-GLUCOSE (GLCn)
3o: ALPHA-D-GLUCOSE (GLCo)
3p: ALPHA-D-GLUCOSE (GLCp)
3q: ALPHA-D-GLUCOSE (GLCq)
3r: ALPHA-D-GLUCOSE (GLCr)
3s: ALPHA-D-GLUCOSE (GLCs)
3t: ALPHA-D-GLUCOSE (GLCt)
3u: ALPHA-D-GLUCOSE (GLCu)
3v: ALPHA-D-GLUCOSE (GLCv)
3w: ALPHA-D-GLUCOSE (GLCw)
3x: ALPHA-D-GLUCOSE (GLCx)
3y: ALPHA-D-GLUCOSE (GLCy)
3z: ALPHA-D-GLUCOSE (GLCz)
4a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
4b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
6i: SULFATE ION (SO4i)
6j: SULFATE ION (SO4j)
6k: SULFATE ION (SO4k)
6l: SULFATE ION (SO4l)
6m: SULFATE ION (SO4m)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
3
GLC
36
Ligand/Ion
ALPHA-D-GLUCOSE
4
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5
NA
2
Ligand/Ion
SODIUM ION
6
SO4
13
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(33, 33)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:424 , GLU A:426 , THR A:443 , GLY A:446 , ASP A:541
BINDING SITE FOR RESIDUE CA A 801
02
AC2
SOFTWARE
ASP A:664 , GLN A:666 , ASN A:669 , HOH A:1202 , HOH A:1391 , HOH A:1403
BINDING SITE FOR RESIDUE NA A 802
03
AC3
SOFTWARE
ARG A:53 , ASN A:55 , LYS A:229 , HOH A:1278 , HOH A:1349 , HOH A:1415
BINDING SITE FOR RESIDUE SO4 A 803
04
AC4
SOFTWARE
PRO A:113 , SER A:114 , HOH A:1161 , HOH A:1502 , HOH A:1591 , ASN B:432 , HOH B:1145 , HOH B:1369
BINDING SITE FOR RESIDUE SO4 A 804
05
AC5
SOFTWARE
THR A:159 , ALA A:160 , HOH A:1351 , HOH A:1477
BINDING SITE FOR RESIDUE SO4 A 805
06
AC6
SOFTWARE
ASN A:345 , ARG A:348
BINDING SITE FOR RESIDUE SO4 A 806
07
AC7
SOFTWARE
ALA A:416 , ARG A:475 , TRP A:509 , HIS A:511 , HOH A:1438
BINDING SITE FOR RESIDUE SO4 A 807
08
AC8
SOFTWARE
GLN A:169 , ASN A:574 , LYS A:594
BINDING SITE FOR RESIDUE SO4 A 808
09
AC9
SOFTWARE
TYR A:530 , VAL A:535 , GLY A:536 , GLC A:825
BINDING SITE FOR RESIDUE SO4 A 809
10
BC1
SOFTWARE
GLU A:241 , ASN A:242 , TYR A:243 , TYR A:276 , HOH A:1370 , SER B:504 , SER B:505
BINDING SITE FOR RESIDUE EDO A 810
11
BC2
SOFTWARE
ARG A:187 , GLU A:241 , ASN A:242 , PRO A:245 , HOH A:1578 , GLY B:197
BINDING SITE FOR RESIDUE EDO A 811
12
BC3
SOFTWARE
GLU A:153 , PHE A:154 , GLU A:155 , ARG A:209 , GLU A:210 , ILE A:211 , HOH A:1586
BINDING SITE FOR RESIDUE EDO A 812
13
BC4
SOFTWARE
GLN A:217 , ASP A:221 , ALA A:300 , GLY A:301 , HOH A:1252 , HOH A:1309
BINDING SITE FOR RESIDUE EDO A 813
14
BC5
SOFTWARE
ALA A:440 , GLY A:441 , TYR A:442
BINDING SITE FOR RESIDUE EDO A 814
15
BC6
SOFTWARE
ARG A:123 , GLN A:131 , GLY A:132 , ASN A:595 , LYS A:598 , ASP A:599 , ASN A:602 , SER A:703 , GLY A:704 , HOH A:1422
BINDING SITE FOR RESIDUE MES A 815
16
BC7
SOFTWARE
GLU B:424 , GLU B:426 , THR B:443 , GLY B:446 , ASP B:541
BINDING SITE FOR RESIDUE CA B 809
17
BC8
SOFTWARE
ASP B:664 , GLN B:666 , ASN B:669 , HOH B:1319 , HOH B:1327 , HOH B:1346
BINDING SITE FOR RESIDUE NA B 810
18
BC9
SOFTWARE
ARG B:53 , ASN B:55 , LYS B:229 , HOH B:1033 , HOH B:1398 , HOH B:1402
BINDING SITE FOR RESIDUE SO4 B 811
19
CC1
SOFTWARE
THR B:159 , ALA B:160 , HOH B:1043 , HOH B:1305 , HOH B:1482
BINDING SITE FOR RESIDUE SO4 B 812
20
CC2
SOFTWARE
ASN B:345 , ARG B:348 , HOH B:1423
BINDING SITE FOR RESIDUE SO4 B 813
21
CC3
SOFTWARE
ARG B:475 , HIS B:511 , HOH B:907
BINDING SITE FOR RESIDUE SO4 B 814
22
CC4
SOFTWARE
GLN B:169 , ASN B:574 , LYS B:594 , HOH B:1494
BINDING SITE FOR RESIDUE SO4 B 815
23
CC5
SOFTWARE
TYR B:530 , VAL B:535 , GLY B:536 , GLC B:830 , HOH B:1085 , HOH B:1282 , HOH B:1471
BINDING SITE FOR RESIDUE SO4 B 816
24
CC6
SOFTWARE
SER B:114 , HOH B:1219
BINDING SITE FOR RESIDUE EDO B 817
25
CC7
SOFTWARE
GLU B:153 , PHE B:154 , GLU B:155 , ARG B:209 , GLU B:210 , HOH B:1492
BINDING SITE FOR RESIDUE EDO B 818
26
CC8
SOFTWARE
PHE B:207 , TYR B:581 , GLC B:829 , HOH B:1514
BINDING SITE FOR RESIDUE EDO B 819
27
CC9
SOFTWARE
ALA B:440 , GLY B:441 , TYR B:442
BINDING SITE FOR RESIDUE EDO B 820
28
DC1
SOFTWARE
ARG B:123 , GLN B:131 , GLY B:132 , ASN B:595 , LYS B:598 , ASP B:599 , ASN B:602 , SER B:703 , GLY B:704
BINDING SITE FOR RESIDUE MES B 821
29
DC2
SOFTWARE
TYR A:182 , ASP A:183 , HIS A:188 , PHE A:207 , TYR A:233 , MET A:235 , VAL A:266 , ASP A:267 , PHE A:268 , GLN A:309 , MET A:310 , GLN A:312 , ARG A:313 , ASN A:354 , VAL A:356 , ASP A:357 , GLU A:380 , TRP A:382 , HIS A:579 , GLU A:580 , TYR A:581 , TYR A:582 , HOH A:1007 , HOH A:1011 , HOH A:1020 , HOH A:1028 , HOH A:1039 , HOH A:1081 , HOH A:1088 , HOH A:1100 , HOH A:1146 , HOH A:1184 , HOH A:1193 , HOH A:1261 , HOH A:1304 , HOH A:1316 , HOH A:1362 , HOH A:1411 , HOH A:1430 , HOH A:1516 , ASN B:262 , GLC B:803 , GLC B:804 , HOH B:1428
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 816 TO 823
30
DC3
SOFTWARE
HIS A:439 , GLN A:450 , ALA A:452 , ASN A:479 , THR A:480 , GLY A:481 , ASN A:539 , THR A:716 , SO4 A:809 , HOH A:1461 , HOH A:1471 , HOH A:1473
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 824 TO 831
31
DC4
SOFTWARE
TYR A:383 , ASP A:386 , THR A:508 , LYS A:510 , GLC A:820 , GLC A:821 , HOH A:1269 , GLU B:241 , ASN B:242 , TYR B:243 , SER B:244 , PRO B:250 , TYR B:255 , SER B:259 , HIS B:260 , THR B:261 , ASN B:262 , TYR B:274 , TYR B:276 , TYR B:319 , HOH B:902 , HOH B:903 , HOH B:904 , HOH B:908 , HOH B:913 , HOH B:1058 , HOH B:1076 , HOH B:1153 , HOH B:1221 , HOH B:1411
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 801 TO 808
32
DC5
SOFTWARE
GLU A:256 , ASP A:257 , ASN A:262 , ASN A:315 , HOH A:1052 , HOH A:1601 , TYR B:182 , ASP B:183 , HIS B:188 , PHE B:207 , TYR B:233 , MET B:235 , VAL B:266 , ASP B:267 , PHE B:268 , GLN B:309 , MET B:310 , GLN B:312 , ARG B:313 , ASN B:354 , VAL B:356 , ASP B:357 , GLU B:380 , TRP B:382 , HIS B:579 , GLU B:580 , TYR B:581 , TYR B:582 , EDO B:819 , HOH B:925 , HOH B:985 , HOH B:986 , HOH B:1000 , HOH B:1013 , HOH B:1056 , HOH B:1132 , HOH B:1163 , HOH B:1174 , HOH B:1243 , HOH B:1256 , HOH B:1268 , HOH B:1292 , HOH B:1295 , HOH B:1321 , HOH B:1382 , HOH B:1399 , HOH B:1428 , HOH B:1488
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 822 TO 829
33
DC6
SOFTWARE
HIS B:439 , ALA B:452 , THR B:480 , TRP B:506 , ASN B:539 , SO4 B:816 , HOH B:1189 , HOH B:1211 , HOH B:1237 , HOH B:1347 , HOH B:1401 , HOH B:1451 , HOH B:1471
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 830 TO 833
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: CBM6 (A:421-546,B:421-546|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CBM6
PS51175
CBM6 (carbohydrate binding type-6) domain profile.
CTA1_BACCI
421-546
748-871
2
A:421-546
B:421-546
-
[
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
(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
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 (270 KB)
Header - Asym.Unit
Biol.Unit 1 (133 KB)
Header - Biol.Unit 1
Biol.Unit 2 (135 KB)
Header - Biol.Unit 2
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
3WNO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
