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.
1H1M
Biol. Unit 2
Info
Asym.Unit (265 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (129 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 QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROL
Authors
:
R. A. Steiner, B. W. Dijkstra
Date
:
19 Jul 02 (Deposition) - 28 Nov 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Oxidoreductase, Dioxygenase, Flavonol
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. A. Steiner, K. H. Kalk, B. W. Dijkstra
Anaerobic Enzyme. Substrate Structures Provide Insight Into The Reaction Mechanism Of The Copper- Dependent Quercetin 2, 3-Dioxygenase.
Proc. Natl. Acad. Sci. Usa V. 99 16625 2002
[
close entry info
]
Hetero Components
(5, 16)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
3a: 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENY... (KMPa)
3b: 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENY... (KMPb)
3c: 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENY... (KMPc)
3d: 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENY... (KMPd)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
5a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
5b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
5c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
5d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6m: N-ACETYL-D-GLUCOSAMINE (NAGm)
6n: N-ACETYL-D-GLUCOSAMINE (NAGn)
6o: N-ACETYL-D-GLUCOSAMINE (NAGo)
6p: N-ACETYL-D-GLUCOSAMINE (NAGp)
6q: N-ACETYL-D-GLUCOSAMINE (NAGq)
6r: N-ACETYL-D-GLUCOSAMINE (NAGr)
6s: N-ACETYL-D-GLUCOSAMINE (NAGs)
6t: N-ACETYL-D-GLUCOSAMINE (NAGt)
6u: N-ACETYL-D-GLUCOSAMINE (NAGu)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CU
-1
Ligand/Ion
COPPER (II) ION
3
KMP
2
Ligand/Ion
3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE
4
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
5
MPD
2
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
6
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC6 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
ARG B:108 , ASN B:109 , HOH B:2080 , HOH B:2377 , HOH B:2378
BINDING SITE FOR RESIDUE NAG B1351
02
AC4
SOFTWARE
LEU A:139 , GLY A:163 , PRO A:164 , THR D:141 , ASN D:142 , HOH D:2166 , HOH D:2359 , HOH D:2360 , HOH D:2361
BINDING SITE FOR RESIDUE NAG D1354
03
AC5
SOFTWARE
ASN D:248 , GLY D:272 , SER D:325 , GLY D:326 , HOH D:2362
BINDING SITE FOR RESIDUE NAG D1355
04
AC7
SOFTWARE
HIS B:66 , HIS B:68 , GLU B:73 , HIS B:112 , KMP B:1358
BINDING SITE FOR RESIDUE CU B1359
05
AC9
SOFTWARE
HIS D:66 , HIS D:68 , GLU D:73 , HIS D:112 , KMP D:1356
BINDING SITE FOR RESIDUE CU D1357
06
BC2
SOFTWARE
MET B:51 , VAL B:63 , HIS B:66 , HIS B:68 , GLU B:73 , PHE B:75 , MET B:123 , GLY B:125 , LEU B:135 , PHE B:136 , LEU B:139 , PRO B:164 , VAL B:177 , CU B:1359 , HOH B:2078 , HOH B:2387
BINDING SITE FOR RESIDUE KMP B1358
07
BC4
SOFTWARE
TYR D:35 , MET D:51 , VAL D:63 , HIS D:66 , HIS D:68 , GLU D:73 , PHE D:75 , PHE D:114 , GLY D:125 , PHE D:132 , LEU D:135 , PHE D:136 , GLY D:163 , PRO D:164 , VAL D:177 , CU D:1357 , HOH D:2085 , HOH D:2363
BINDING SITE FOR RESIDUE KMP D1356
08
BC6
SOFTWARE
GLN B:117 , ASP B:118 , MPD B:1361 , VAL D:97 , SER D:99 , ASP D:102 , HIS D:201
BINDING SITE FOR RESIDUE MPD B1360
09
BC7
SOFTWARE
VAL B:97 , SER B:99 , ASP B:102 , HIS B:201 , MPD B:1360 , SER D:81 , GLN D:117 , ASP D:118
BINDING SITE FOR RESIDUE MPD B1361
10
BC9
SOFTWARE
ASN A:90 , THR A:141 , ASN A:142 , ASN A:191 , ASN A:248 , GLY A:272 , SER A:325 , GLY A:326 , HOH A:2128 , HOH A:2404 , HOH A:2405 , HOH A:2407 , HOH A:2409 , HOH A:2410 , HOH A:2412 , HOH A:2414 , GLN C:83 , THR C:184 , THR C:187 , ASP C:188 , THR C:189 , LEU D:139 , GLY D:163 , PRO D:164 , HOH D:2186
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 191 RESIDUES 1352 TO 1359
11
CC1
SOFTWARE
ARG B:26 , ASN B:142 , VAL B:190 , ASN B:191 , ASN B:248 , GLY B:272 , SER B:325 , GLY B:326 , HOH B:2155 , HOH B:2379 , HOH B:2380 , HOH B:2381 , HOH B:2382 , HOH B:2383 , HOH B:2384 , HOH B:2385 , HOH B:2386 , NAG C:1355 , GLN D:83 , THR D:187 , THR D:189 , HOH D:2208 , HOH D:2212
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 191 RESIDUES 1352 TO 1357
12
CC2
SOFTWARE
GLN A:83 , THR A:187 , ASP A:188 , THR A:189 , HOH A:2235 , ARG B:26 , NAG B:1355 , HOH B:2384 , ASN C:142 , VAL C:190 , ASN C:191 , ASN C:248 , GLY C:272 , SER C:325 , GLY C:326 , HOH C:2057 , HOH C:2221 , HOH C:2372 , HOH C:2373 , HOH C:2374 , HOH C:2377 , HOH C:2378 , HOH C:2380
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 191 RESIDUES 1352 TO 1357
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1h1ma_ (A:)
1b: SCOP_d1h1mb_ (B:)
1c: SCOP_d1h1mc_ (C:)
1d: SCOP_d1h1md_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
RmlC-like cupins
(220)
Family
:
Quercetin 2,3-dioxygenase-like
(7)
Protein domain
:
Quercetin 2,3-dioxygenase
(5)
Aspergillus japonicus [TaxId: 34381]
(5)
1a
d1h1ma_
A:
1b
d1h1mb_
B:
1c
d1h1mc_
C:
1d
d1h1md_
D:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1h1mB02 (B:206-350)
1b: CATH_1h1mA01 (A:3-21,A:222-342)
1c: CATH_1h1mB01 (B:3-145)
1d: CATH_1h1mC01 (C:3-145)
1e: CATH_1h1mD01 (D:4-145)
1f: CATH_1h1mA02 (A:22-221)
1g: CATH_1h1mC02 (C:206-350)
1h: CATH_1h1mD02 (D:206-350)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Jelly Rolls
(177)
Aspergillus japonicus. Organism_taxid: 34381.
(4)
1a
1h1mB02
B:206-350
1b
1h1mA01
A:3-21,A:222-342
1c
1h1mB01
B:3-145
1d
1h1mC01
C:3-145
1e
1h1mD01
D:4-145
1f
1h1mA02
A:22-221
1g
1h1mC02
C:206-350
1h
1h1mD02
D:206-350
[
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 B
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 (265 KB)
Header - Asym.Unit
Biol.Unit 1 (132 KB)
Header - Biol.Unit 1
Biol.Unit 2 (129 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
1H1M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
