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1H1M
Asym. Unit
Info
Asym.Unit (265 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (129 KB)
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(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
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Hetero Components
(6, 40)
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
3
Ligand/Ion
BETA-D-MANNOSE
2
CU
4
Ligand/Ion
COPPER (II) ION
3
KMP
4
Ligand/Ion
3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
MPD
4
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
6
NAG
21
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:69 , ARG A:108 , ASN A:109 , HOH A:2095 , HOH A:2403
BINDING SITE FOR RESIDUE NAG A1351
02
AC2
SOFTWARE
ARG B:108 , ASN B:109 , HOH B:2080 , HOH B:2377 , HOH B:2378
BINDING SITE FOR RESIDUE NAG B1351
03
AC3
SOFTWARE
ARG C:108 , ASN C:109 , HOH C:2106 , HOH C:2370
BINDING SITE FOR RESIDUE NAG C1351
04
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
05
AC5
SOFTWARE
ASN D:248 , GLY D:272 , SER D:325 , GLY D:326 , HOH D:2362
BINDING SITE FOR RESIDUE NAG D1355
06
AC6
SOFTWARE
HIS A:66 , HIS A:68 , GLU A:73 , HIS A:112 , KMP A:1360
BINDING SITE FOR RESIDUE CU A1361
07
AC7
SOFTWARE
HIS B:66 , HIS B:68 , GLU B:73 , HIS B:112 , KMP B:1358
BINDING SITE FOR RESIDUE CU B1359
08
AC8
SOFTWARE
HIS C:66 , HIS C:68 , GLU C:73 , HIS C:112 , KMP C:1358
BINDING SITE FOR RESIDUE CU C1359
09
AC9
SOFTWARE
HIS D:66 , HIS D:68 , GLU D:73 , HIS D:112 , KMP D:1356
BINDING SITE FOR RESIDUE CU D1357
10
BC1
SOFTWARE
MET A:51 , VAL A:63 , HIS A:66 , HIS A:68 , GLU A:73 , PHE A:75 , PHE A:114 , GLY A:125 , PHE A:132 , LEU A:135 , PHE A:136 , LEU A:139 , GLY A:163 , PRO A:164 , VAL A:177 , CU A:1361 , HOH A:2415 , HOH A:2416
BINDING SITE FOR RESIDUE KMP A1360
11
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
12
BC3
SOFTWARE
TYR C:35 , MET C:51 , VAL C:63 , HIS C:66 , HIS C:68 , GLU C:73 , PHE C:75 , MET C:123 , GLY C:125 , PHE C:132 , LEU C:135 , PHE C:136 , LEU C:139 , PRO C:164 , VAL C:177 , CU C:1359 , HOH C:2098 , HOH C:2381
BINDING SITE FOR RESIDUE KMP C1358
13
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
14
BC5
SOFTWARE
VAL A:97 , SER A:99 , ASP A:102 , TRP A:200 , HIS A:201 , SER C:81 , GLN C:117 , ASP C:118 , MPD C:1360
BINDING SITE FOR RESIDUE MPD A1362
15
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
16
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
17
BC8
SOFTWARE
GLN A:117 , ASP A:118 , MPD A:1362 , VAL C:97 , SER C:99 , ASP C:102 , HIS C:201
BINDING SITE FOR RESIDUE MPD C1360
18
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
19
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
20
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
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1h1ma_ (A:)
1b: SCOP_d1h1mb_ (B:)
1c: SCOP_d1h1mc_ (C:)
1d: SCOP_d1h1md_ (D:)
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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)
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Topologies
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(
)
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
[
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]
Pfam Domains
(0, 0)
Info
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