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.
2Z8G
Biol. Unit 2
Info
Asym.Unit (210 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (103 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ASPERGILLUS NIGER ATCC9642 ISOPULLULANASE COMPLEXED WITH ISOPANOSE
Authors
:
M. Mizuno, A. Koide, A. Yamamura, H. Akeboshi, H. Yoshida, S. Kamitori, A. Nishikawa, T. Tonozuka
Date
:
05 Sep 07 (Deposition) - 18 Dec 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Isopullulanase, Gh49, Dextranase, Pullulan, Beta-Helix, Glycoprotein, Glycosidase, Hydrolase, Secreted
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Mizuno, A. Koide, A. Yamamura, H. Akeboshi, H. Yoshida, S. Kamitori Y. Sakano, A. Nishikawa, T. Tonozuka
Crystal Structure Of Aspergillus Niger Isopullulanase, A Member Of Glycoside Hydrolase Family 49
J. Mol. Biol. V. 376 210 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
2a: ALPHA-D-GLUCOSE (GLCa)
2b: ALPHA-D-GLUCOSE (GLCb)
2c: ALPHA-D-GLUCOSE (GLCc)
2d: ALPHA-D-GLUCOSE (GLCd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
2
GLC
2
Ligand/Ion
ALPHA-D-GLUCOSE
3
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(21, 21)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC8 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC7 (SOFTWARE)
18: CC8 (SOFTWARE)
19: CC9 (SOFTWARE)
20: DC1 (SOFTWARE)
21: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
LEU A:54 , ARG A:114 , ASN A:115 , SER A:118 , HOH A:1370 , HOH A:1610 , GLY B:304 , ASN B:305
BINDING SITE FOR RESIDUE NAG A 1002
02
AC4
SOFTWARE
ASN A:210 , ASP A:230 , HOH A:1082 , HOH A:1117 , HOH A:1222 , HOH A:1362 , HOH A:1540 , HOH A:1631 , ASN B:138 , GLN B:139
BINDING SITE FOR RESIDUE NAG A 1003
03
AC5
SOFTWARE
ASN A:305 , HOH A:1211 , HOH A:1391 , THR B:40 , GLN B:41 , NAG B:1002
BINDING SITE FOR RESIDUE NAG A 1004
04
AC6
SOFTWARE
ASN A:381 , HOH A:1392 , SER B:26 , PHE B:184
BINDING SITE FOR RESIDUE NAG A 1005
05
AC8
SOFTWARE
ASN A:409 , ASN A:460 , HOH A:1208 , HOH A:1532 , TYR B:147
BINDING SITE FOR RESIDUE NAG A 1007
06
BC1
SOFTWARE
ALA A:425 , ASN A:503 , HOH A:1354 , HOH A:1357 , HOH B:1249
BINDING SITE FOR RESIDUE NAG A 1009
07
BC2
SOFTWARE
ASN A:535 , HOH A:1385 , HOH A:1482 , ASN B:120 , SER B:121 , ASN B:122 , TYR B:136 , HOH B:1415
BINDING SITE FOR RESIDUE NAG A 1010
08
BC4
SOFTWARE
ASN B:24 , PRO B:221 , HOH B:1388
BINDING SITE FOR RESIDUE NAG B 1000
09
BC8
SOFTWARE
ASN B:94 , SER B:164 , GLU B:174 , HOH B:1211 , HOH B:1231 , HOH B:1248 , HOH B:1413 , HOH B:1448
BINDING SITE FOR RESIDUE NAG B 1001
10
BC9
SOFTWARE
NAG A:1004 , LEU B:54 , ARG B:114 , ASN B:115 , SER B:118 , HOH B:1349
BINDING SITE FOR RESIDUE NAG B 1002
11
CC1
SOFTWARE
HIS A:231 , GLU A:254 , PRO A:281 , TYR A:285 , HOH A:1315 , HOH A:1406 , ASN B:138 , HOH B:1220
BINDING SITE FOR RESIDUE NAG B 1003
12
CC2
SOFTWARE
GLN A:139 , LEU B:207 , ASN B:210 , ASP B:230 , HOH B:1121 , HOH B:1145 , HOH B:1157 , HOH B:1463
BINDING SITE FOR RESIDUE NAG B 1004
13
CC3
SOFTWARE
GLN A:27 , HIS A:106 , HOH A:1633 , ASN B:305 , HOH B:1471
BINDING SITE FOR RESIDUE NAG B 1005
14
CC4
SOFTWARE
ASN B:381 , HOH B:1434 , HOH B:1440
BINDING SITE FOR RESIDUE NAG B 1006
15
CC5
SOFTWARE
TYR B:440 , ASN B:448 , THR B:451 , HOH B:1303
BINDING SITE FOR RESIDUE NAG B 1007
16
CC6
SOFTWARE
GLY B:452 , ASN B:453 , ASN B:455 , ASP B:514 , ASN B:516 , HOH B:1475
BINDING SITE FOR RESIDUE NAG B 1008
17
CC7
SOFTWARE
ASN B:409 , ASN B:460 , HOH B:1140 , HOH B:1177 , HOH B:1230 , HOH B:1387
BINDING SITE FOR RESIDUE NAG B 1009
18
CC8
SOFTWARE
ASN B:465 , LYS B:490 , ASN B:491 , HOH B:1128 , HOH B:1280 , HOH B:1379
BINDING SITE FOR RESIDUE NAG B 1010
19
CC9
SOFTWARE
ASP B:372 , VAL B:394 , TRP B:402 , ASN B:428 , PRO B:442 , ASP B:443 , HOH B:683 , HOH B:1130 , HOH B:1522 , GLC B:2002
BINDING SITE FOR RESIDUE GLC B 2001
20
DC1
SOFTWARE
VAL B:394 , GLY B:426 , ASN B:427 , HOH B:1523 , GLC B:2001 , BGC B:2003
BINDING SITE FOR RESIDUE GLC B 2002
21
DC2
SOFTWARE
HOH A:1468 , GLN B:88 , TYR B:89 , THR B:90 , GLN B:91 , GLY B:350 , HOH B:1521 , HOH B:1524 , HOH B:1525 , HOH B:1526 , GLC B:2002
BINDING SITE FOR RESIDUE BGC B 2003
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2z8gA02 (A:191-564)
1b: CATH_2z8gB02 (B:191-564)
2a: CATH_2z8gA01 (A:19-189)
2b: CATH_2z8gB01 (B:19-189)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
3 Solenoid
(196)
Topology
:
Pectate Lyase C-like
(105)
Homologous Superfamily
:
Single-stranded right-handed beta-helix, Pectin lyase-like
(73)
Aspergillus niger. Organism_taxid: 5061. Strain: atcc9642.
(1)
1a
2z8gA02
A:191-564
1b
2z8gB02
B:191-564
Architecture
:
Sandwich
(5577)
Topology
:
Dex49a from penicillium minioluteum complex, domain 1
(5)
Homologous Superfamily
:
Dex49a from penicillium minioluteum complex, domain 1
(5)
Aspergillus niger. Organism_taxid: 5061. Strain: atcc9642.
(1)
2a
2z8gA01
A:19-189
2b
2z8gB01
B:19-189
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_49_2z8gB01 (B:20-563)
1b: PFAM_Glyco_hydro_49_2z8gB02 (B:20-563)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Pec_lyase
(42)
Family
:
Glyco_hydro_49
(3)
Aspergillus niger
(3)
1a
Glyco_hydro_49-2z8gB01
B:20-563
1b
Glyco_hydro_49-2z8gB02
B:20-563
[
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 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 (210 KB)
Header - Asym.Unit
Biol.Unit 1 (105 KB)
Header - Biol.Unit 1
Biol.Unit 2 (103 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
2Z8G
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help