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1H1I
Biol. Unit 1
Info
Asym.Unit (262 KB)
Biol.Unit 1 (130 KB)
Biol.Unit 2 (128 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE QUERCETN
Authors
:
R. A. Steiner, B. W. Dijkstra
Date
:
15 Jul 02 (Deposition) - 28 Nov 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
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
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Hetero Components
(3, 15)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
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)
4a: 3,5,7,3',4'-PENTAHYDROXYFLAVONE (QUEa)
4b: 3,5,7,3',4'-PENTAHYDROXYFLAVONE (QUEb)
4c: 3,5,7,3',4'-PENTAHYDROXYFLAVONE (QUEc)
4d: 3,5,7,3',4'-PENTAHYDROXYFLAVONE (QUEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
-1
Ligand/Ion
COPPER (II) ION
2
MPD
2
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
QUE
2
Ligand/Ion
3,5,7,3',4'-PENTAHYDROXYFLAVONE
[
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Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC8 (SOFTWARE)
13: CC1 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC8 (SOFTWARE)
17: CC9 (SOFTWARE)
18: DC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:108 , ASN A:109 , HOH A:2095 , HOH A:2415
BINDING SITE FOR RESIDUE NAG A1351
02
AC2
SOFTWARE
ASN A:248 , GLY A:272 , SER A:325 , GLY A:326 , HOH A:2418 , HOH A:2419 , HOH A:2420
BINDING SITE FOR RESIDUE NAG A1354
03
AC3
SOFTWARE
ASN A:90 , HOH A:2421
BINDING SITE FOR RESIDUE NAG A1355
04
AC4
SOFTWARE
THR A:141 , ASN A:142 , HOH A:2422 , HOH A:2423 , HOH A:2424 , HOH A:2425 , LEU D:139 , GLY D:163 , PRO D:164
BINDING SITE FOR RESIDUE NAG A1356
05
AC8
SOFTWARE
ARG B:26 , ASN B:142 , HOH B:2376 , NAG C:1356
BINDING SITE FOR RESIDUE NAG B1354
06
AC9
SOFTWARE
ARG C:108 , ASN C:109 , HOH C:2102 , HOH C:2363
BINDING SITE FOR RESIDUE NAG C1352
07
BC1
SOFTWARE
ASN C:248 , GLY C:272 , SER C:325 , GLY C:326
BINDING SITE FOR RESIDUE NAG C1355
08
BC2
SOFTWARE
NAG B:1354 , ARG C:26 , ASN C:142 , HOH C:2367 , HOH C:2368
BINDING SITE FOR RESIDUE NAG C1356
09
BC3
SOFTWARE
SER A:182 , ARG D:108 , ASN D:109 , HOH D:2358
BINDING SITE FOR RESIDUE NAG D1351
10
BC4
SOFTWARE
LEU A:139 , GLY A:163 , PRO A:164 , HOH A:2062 , THR D:141 , ASN D:142 , HOH D:2360 , HOH D:2361
BINDING SITE FOR RESIDUE NAG D1354
11
BC6
SOFTWARE
HIS A:66 , HIS A:68 , GLU A:73 , HIS A:112 , QUE A:1358
BINDING SITE FOR RESIDUE CU A1357
12
BC8
SOFTWARE
HIS C:66 , HIS C:68 , GLU C:73 , HIS C:112 , QUE C:1358
BINDING SITE FOR RESIDUE CU C1357
13
CC1
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 , GLY A:163 , PRO A:164 , VAL A:177 , CU A:1357 , HOH A:2426 , HOH A:2427
BINDING SITE FOR RESIDUE QUE A1358
14
CC3
SOFTWARE
TYR C:35 , MET C:51 , VAL C:63 , HIS C:66 , HIS C:68 , GLU C:73 , PHE C:75 , PHE C:114 , MET C:123 , GLY C:125 , LEU C:135 , PHE C:136 , LEU C:139 , GLY C:163 , PRO C:164 , VAL C:177 , CU C:1357 , HOH C:2369 , HOH C:2370
BINDING SITE FOR RESIDUE QUE C1358
15
CC5
SOFTWARE
VAL A:97 , SER A:99 , ASP A:102 , TRP A:200 , HIS A:201 , GLN C:117 , ASP C:118 , MPD C:1351
BINDING SITE FOR RESIDUE MPD A1359
16
CC8
SOFTWARE
SER A:81 , GLN A:117 , ASP A:118 , MPD A:1359 , VAL C:97 , SER C:99 , ASP C:102 , HIS C:201
BINDING SITE FOR RESIDUE MPD C1351
17
CC9
SOFTWARE
ASN A:191 , HOH A:2239 , HOH A:2416 , HOH A:2417 , GLN C:83 , THR C:187 , ASP C:188 , THR C:189
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 191 RESIDUES 1352 TO 1353
18
DC1
SOFTWARE
GLN A:83 , THR A:187 , ASP A:188 , THR A:189 , HOH A:2234 , ASN C:191 , HOH C:2220 , HOH C:2365
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 191 RESIDUES 1353 TO 1354
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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Exons
(0, 0)
Info
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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_d1h1ia_ (A:)
1b: SCOP_d1h1ic_ (C:)
1c: SCOP_d1h1id_ (D:)
1d: SCOP_d1h1ib_ (B:)
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(
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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
d1h1ia_
A:
1b
d1h1ic_
C:
1c
d1h1id_
D:
1d
d1h1ib_
B:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1h1iA02 (A:206-350)
1b: CATH_1h1iB01 (B:3-21,B:222-342)
1c: CATH_1h1iA01 (A:3-145)
1d: CATH_1h1iC01 (C:3-145)
1e: CATH_1h1iD01 (D:4-145)
1f: CATH_1h1iB02 (B:22-221)
1g: CATH_1h1iC02 (C:206-350)
1h: CATH_1h1iD02 (D:206-350)
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Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Jelly Rolls
(177)
Aspergillus japonicus. Organism_taxid: 34381.
(4)
1a
1h1iA02
A:206-350
1b
1h1iB01
B:3-21,B:222-342
1c
1h1iA01
A:3-145
1d
1h1iC01
C:3-145
1e
1h1iD01
D:4-145
1f
1h1iB02
B:22-221
1g
1h1iC02
C:206-350
1h
1h1iD02
D:206-350
[
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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