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3AM9
Asym. Unit
Info
Asym.Unit (456 KB)
Biol.Unit 1 (446 KB)
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(1)
Title
:
COMPLEX OF BOVINE XANTHINE DEHYDROGENASE AND TRIHYDROXY FYX-051
Authors
:
K. Matsumoto, K. Okamoto, N. Ashizawa, T. Matsumura, T. Kusano, T. Nish
Date
:
18 Aug 10 (Deposition) - 03 Nov 10 (Release) - 29 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.17
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Xanthine Oxidoreductase, Xanthine Dehydrogenase, Fyx-051, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Matsumoto, K. Okamoto, N. Ashizawa, T. Nishino
Fyx-051: A Novel And Potent Hybrid-Type Inhibitor Of Xanthine Oxidoreductase
J. Pharmacol. Exp. Ther. V. 336 95 2011
[
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Hetero Components
(8, 20)
Info
All Hetero Components
1a: BICARBONATE ION (BCTa)
1b: BICARBONATE ION (BCTb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
4b: FE2/S2 (INORGANIC) CLUSTER (FESb)
4c: FE2/S2 (INORGANIC) CLUSTER (FESc)
4d: FE2/S2 (INORGANIC) CLUSTER (FESd)
5a: 4-[5-(2,6-DIOXO-1,2,3,6-TETRAHYDRO... (FYOa)
5b: 4-[5-(2,6-DIOXO-1,2,3,6-TETRAHYDRO... (FYOb)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
7a: DIOXOTHIOMOLYBDENUM(VI) ION (MOSa)
7b: DIOXOTHIOMOLYBDENUM(VI) ION (MOSb)
8a: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEa)
8b: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCT
2
Ligand/Ion
BICARBONATE ION
2
CA
4
Ligand/Ion
CALCIUM ION
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
FYO
2
Ligand/Ion
4-[5-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIDIN-4-YL)-1H-1,2,4-TRIAZOL-3-YL]-6-OXO-1,6-DIHYDROPYRIDINE-2-CARBONITRILE
6
GOL
2
Ligand/Ion
GLYCEROL
7
MOS
2
Ligand/Ion
DIOXOTHIOMOLYBDENUM(VI) ION
8
MTE
2
Ligand/Ion
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
[
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]
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:112 , CYS A:113 , GLY A:114 , CYS A:116 , CYS A:148 , ARG A:149 , CYS A:150
BINDING SITE FOR RESIDUE FES A 3001
02
AC2
SOFTWARE
GLY A:42 , CYS A:43 , GLY A:44 , GLY A:46 , GLY A:47 , CYS A:48 , GLY A:49 , CYS A:51 , ASN A:71 , CYS A:73
BINDING SITE FOR RESIDUE FES A 3002
03
AC3
SOFTWARE
ALA A:867 , SER A:870 , ARG A:871 , SER A:874 , SER A:907 , ASN A:908
BINDING SITE FOR RESIDUE CA A 3008
04
AC4
SOFTWARE
GLU A:45 , GLY A:46 , LYS A:256 , LEU A:257 , VAL A:259 , GLY A:260 , ASN A:261 , THR A:262 , GLU A:263 , ILE A:264 , ALA A:301 , PHE A:337 , ALA A:338 , VAL A:342 , ALA A:346 , SER A:347 , GLY A:350 , ASN A:351 , ILE A:353 , THR A:354 , SER A:359 , ASP A:360 , LEU A:404 , LYS A:422 , ASP A:429 , ASP A:430 , HOH A:1483 , HOH A:1582 , HOH A:1609 , HOH A:1895 , HOH A:2074
BINDING SITE FOR RESIDUE FAD A 3005
05
AC5
SOFTWARE
ARG A:839 , HIS A:840 , ILE A:877 , THR A:909 , ALA A:910 , PHE A:911 , PHE A:914 , GLY A:915 , GLN A:918
BINDING SITE FOR RESIDUE BCT A 1904
06
AC6
SOFTWARE
GLN A:112 , CYS A:150 , GLY A:796 , GLY A:797 , PHE A:798 , GLY A:799 , ARG A:912 , MET A:1038 , GLY A:1039 , GLN A:1040 , ALA A:1079 , SER A:1080 , VAL A:1081 , SER A:1082 , GLN A:1194 , GLU A:1261 , MOS A:1334 , FYO A:1335 , HOH A:1677 , HOH A:2293 , HOH A:2294
BINDING SITE FOR RESIDUE MTE A 1333
07
AC7
SOFTWARE
GLN A:767 , GLY A:799 , GLU A:802 , PHE A:911 , ARG A:912 , GLU A:1261 , MTE A:1333 , FYO A:1335
BINDING SITE FOR RESIDUE MOS A 1334
08
AC8
SOFTWARE
LEU A:648 , GLU A:802 , LEU A:873 , SER A:876 , ARG A:880 , PHE A:914 , PHE A:1009 , LEU A:1014 , ALA A:1079 , GLU A:1261 , MTE A:1333 , MOS A:1334 , HOH A:2289 , HOH A:2291
BINDING SITE FOR RESIDUE FYO A 1335
09
AC9
SOFTWARE
HIS A:741 , TYR A:743 , THR A:836 , GLY A:837 , HOH A:2311
BINDING SITE FOR RESIDUE CA A 1336
10
BC1
SOFTWARE
GLN B:112 , CYS B:113 , GLY B:114 , CYS B:116 , CYS B:148 , ARG B:149 , CYS B:150
BINDING SITE FOR RESIDUE FES B 4001
11
BC2
SOFTWARE
GLY B:42 , CYS B:43 , GLY B:44 , GLY B:46 , GLY B:47 , CYS B:48 , GLY B:49 , CYS B:51 , ASN B:71 , CYS B:73
BINDING SITE FOR RESIDUE FES B 4002
12
BC3
SOFTWARE
ALA B:867 , SER B:870 , ARG B:871 , SER B:874 , SER B:907 , ASN B:908
BINDING SITE FOR RESIDUE CA B 4008
13
BC4
SOFTWARE
GLU B:45 , GLY B:46 , LYS B:256 , LEU B:257 , VAL B:258 , VAL B:259 , GLY B:260 , ASN B:261 , THR B:262 , GLU B:263 , ILE B:264 , ALA B:301 , PHE B:337 , ALA B:338 , SER B:347 , GLY B:350 , ASN B:351 , ILE B:353 , THR B:354 , SER B:359 , ASP B:360 , ILE B:403 , LEU B:404 , LYS B:422 , ASP B:429 , ASP B:430 , HOH B:1713 , HOH B:1867 , HOH B:2068
BINDING SITE FOR RESIDUE FAD B 4005
14
BC5
SOFTWARE
ARG B:839 , HIS B:840 , ILE B:877 , THR B:909 , ALA B:910 , PHE B:911 , PHE B:914 , GLY B:915 , GLN B:918
BINDING SITE FOR RESIDUE BCT B 1904
15
BC6
SOFTWARE
GLN B:112 , CYS B:150 , GLY B:796 , GLY B:797 , PHE B:798 , GLY B:799 , ARG B:912 , MET B:1038 , GLY B:1039 , GLN B:1040 , ALA B:1078 , ALA B:1079 , SER B:1080 , VAL B:1081 , SER B:1082 , GLN B:1194 , GLU B:1261 , MOS B:1334 , FYO B:1335 , HOH B:1386 , HOH B:2248 , HOH B:2249
BINDING SITE FOR RESIDUE MTE B 1333
16
BC7
SOFTWARE
GLN B:767 , GLY B:799 , PHE B:911 , ARG B:912 , GLU B:1261 , MTE B:1333 , FYO B:1335
BINDING SITE FOR RESIDUE MOS B 1334
17
BC8
SOFTWARE
LEU B:648 , GLU B:802 , LEU B:873 , SER B:876 , ARG B:880 , PHE B:914 , PHE B:1009 , VAL B:1011 , LEU B:1014 , ALA B:1078 , ALA B:1079 , GLU B:1261 , MTE B:1333 , MOS B:1334 , HOH B:1848 , HOH B:2247
BINDING SITE FOR RESIDUE FYO B 1335
18
BC9
SOFTWARE
HIS B:665 , ILE B:666 , ARG B:804 , ILE B:835 , ASN B:869 , SER B:906 , SER B:907 , HOH B:1557 , HOH B:1602
BINDING SITE FOR RESIDUE GOL B 1336
19
CC1
SOFTWARE
HIS B:741 , TYR B:743 , THR B:836 , GLY B:837 , HOH B:2257
BINDING SITE FOR RESIDUE CA B 1337
20
CC2
SOFTWARE
ASP B:594 , PHE B:604 , ARG B:824 , MET B:826 , HOH B:1352
BINDING SITE FOR RESIDUE GOL B 1338
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (A:4-91,B:4-91)
2: 2FE2S_FER_1 (A:43-51,B:43-51)
3: FAD_PCMH (A:229-414,B:229-414)
4: MOLYBDOPTERIN_EUK (A:797-832,B:797-832)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
XDH_BOVIN
4-91
2
A:4-91
B:4-91
2
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
XDH_BOVIN
43-51
2
A:43-51
B:43-51
3
FAD_PCMH
PS51387
PCMH-type FAD-binding domain profile.
XDH_BOVIN
229-414
2
A:229-414
B:229-414
4
MOLYBDOPTERIN_EUK
PS00559
Eukaryotic molybdopterin oxidoreductases signature.
XDH_BOVIN
797-832
2
A:797-832
B:797-832
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(6, 12)
Info
All SCOP Domains
1a: SCOP_d3am9a2 (A:93-165)
1b: SCOP_d3am9b2 (B:93-165)
2a: SCOP_d3am9a5 (A:537-694)
2b: SCOP_d3am9b5 (B:537-694)
3a: SCOP_d3am9a1 (A:3-92)
3b: SCOP_d3am9b1 (B:3-92)
4a: SCOP_d3am9a4 (A:415-530)
4b: SCOP_d3am9b4 (B:415-528)
5a: SCOP_d3am9a3 (A:192-414)
5b: SCOP_d3am9b3 (B:192-414)
6a: SCOP_d3am9a6 (A:695-1332)
6b: SCOP_d3am9b6 (B:695-1332)
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Classes
(
)
(
)
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(
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(
)
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
CO dehydrogenase ISP C-domain like
(45)
Superfamily
:
CO dehydrogenase ISP C-domain like
(45)
Family
:
CO dehydrogenase ISP C-domain like
(42)
Protein domain
:
Xanthine oxidase, domain 2
(11)
Cow (Bos taurus) [TaxId: 9913]
(11)
1a
d3am9a2
A:93-165
1b
d3am9b2
B:93-165
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
CO dehydrogenase molybdoprotein N-domain-like
(44)
Family
:
CO dehydrogenase molybdoprotein N-domain-like
(34)
Protein domain
:
Xanthine oxidase, domain 5 (?)
(11)
Cow (Bos taurus) [TaxId: 9913]
(11)
2a
d3am9a5
A:537-694
2b
d3am9b5
B:537-694
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Xanthine oxidase, N-terminal domain
(11)
Cow (Bos taurus) [TaxId: 9913]
(11)
3a
d3am9a1
A:3-92
3b
d3am9b1
B:3-92
Fold
:
CO dehydrogenase flavoprotein C-domain-like
(111)
Superfamily
:
CO dehydrogenase flavoprotein C-terminal domain-like
(35)
Family
:
CO dehydrogenase flavoprotein C-terminal domain-like
(23)
Protein domain
:
Xanthine oxidase, domain 4 (?)
(10)
Cow (Bos taurus) [TaxId: 9913]
(10)
4a
d3am9a4
A:415-530
4b
d3am9b4
B:415-528
Fold
:
FAD-binding/transporter-associated domain-like
(99)
Superfamily
:
FAD-binding/transporter-associated domain-like
(99)
Family
:
CO dehydrogenase flavoprotein N-terminal domain-like
(33)
Protein domain
:
Xanthine oxidase, domain 3 (?)
(10)
Cow (Bos taurus) [TaxId: 9913]
(10)
5a
d3am9a3
A:192-414
5b
d3am9b3
B:192-414
Fold
:
Molybdenum cofactor-binding domain
(44)
Superfamily
:
Molybdenum cofactor-binding domain
(44)
Family
:
Molybdenum cofactor-binding domain
(44)
Protein domain
:
Xanthine oxidase, C-terminal domain
(11)
Cow (Bos taurus) [TaxId: 9913]
(11)
6a
d3am9a6
A:695-1332
6b
d3am9b6
B:695-1332
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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