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1V97
Asym. Unit
Info
Asym.Unit (461 KB)
Biol.Unit 1 (452 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE MILK XANTHINE DEHYDROGENASE FYX-051 BOUND FORM
Authors
:
K. Okamoto, K. Matsumoto, R. Hille, B. T. Eger, E. F. Pai, T. Nishino
Date
:
21 Jan 04 (Deposition) - 22 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.94
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Xanthine Dehydrogenase, Molybdopterin, Fyx-051, Reaction Intermediate, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Okamoto, K. Matsumoto, R. Hille, B. T. Eger, E. F. Pai, T. Nishino
The Crystal Structure Of Xanthine Oxidoreductase During Catalysis: Implications For Reaction Mechanism And Enzyme Inhibition.
Proc. Natl. Acad. Sci. Usa V. 101 7931 2004
[
close entry info
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Hetero Components
(8, 24)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
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-PYRIDIN-4-YL-1H-1,2,4-TRIAZOL... (FYXa)
5b: 4-(5-PYRIDIN-4-YL-1H-1,2,4-TRIAZOL... (FYXb)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
6g: GLYCEROL (GOLg)
6h: GLYCEROL (GOLh)
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
ACY
2
Ligand/Ion
ACETIC ACID
2
CA
2
Ligand/Ion
CALCIUM ION
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
FYX
2
Ligand/Ion
4-(5-PYRIDIN-4-YL-1H-1,2,4-TRIAZOL-3-YL)PYRIDINE-2-CARBONITRILE
6
GOL
8
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
[
close Hetero Component info
]
Sites
(24, 24)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
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
02
AC2
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
03
AC3
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
04
AC4
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
05
AC5
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:1078 , ALA A:1079 , SER A:1080 , VAL A:1081 , SER A:1082 , GLN A:1194 , GLU A:1261 , MOS A:3004 , HOH A:5020 , HOH A:5028 , HOH A:5052 , HOH A:5111
BINDING SITE FOR RESIDUE MTE A 3003
06
AC6
SOFTWARE
GLN A:767 , GLY A:799 , PHE A:911 , ARG A:912 , ALA A:1078 , ALA A:1079 , GLU A:1261 , MTE A:3003 , FYX A:3006
BINDING SITE FOR RESIDUE MOS A 3004
07
AC7
SOFTWARE
GLU A:45 , GLY A:46 , LYS A:256 , LEU A:257 , VAL A:258 , 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 , ALA A:346 , SER A:347 , GLY A:350 , ASN A:351 , ILE A:353 , THR A:354 , SER A:359 , ASP A:360 , ILE A:403 , LEU A:404 , LYS A:422 , ASP A:429 , HOH A:5200 , HOH A:5235 , HOH A:5241 , HOH A:5364 , HOH A:5379 , HOH A:5584 , HOH A:6010 , HOH A:6062
BINDING SITE FOR RESIDUE FAD A 3005
08
AC8
SOFTWARE
ASN A:768 , LYS A:771 , GLU A:802 , LEU A:873 , ARG A:880 , PHE A:914 , PHE A:1009 , LEU A:1014 , ALA A:1079 , GLU A:1261 , MOS A:3004 , HOH A:5593 , HOH A:5936
BINDING SITE FOR RESIDUE FYX A 3006
09
AC9
SOFTWARE
GLN B:112 , CYS B:113 , GLY B:114 , CYS B:116 , CYS B:148 , ARG B:149 , CYS B:150 , LEU B:744
BINDING SITE FOR RESIDUE FES B 4001
10
BC1
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
11
BC2
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:4004 , HOH B:5063 , HOH B:5065 , HOH B:5104
BINDING SITE FOR RESIDUE MTE B 4003
12
BC3
SOFTWARE
GLN B:767 , GLY B:799 , PHE B:911 , ARG B:912 , ALA B:1078 , ALA B:1079 , GLU B:1261 , MTE B:4003 , FYX B:4006
BINDING SITE FOR RESIDUE MOS B 4004
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 , ALA B:346 , SER B:347 , GLY B:350 , ASN B:351 , ILE B:353 , THR B:354 , SER B:359 , ASP B:360 , LEU B:404 , LYS B:422 , ASP B:429 , ASP B:430 , HOH B:5126 , HOH B:5191 , HOH B:5240 , HOH B:5252 , HOH B:5273 , HOH B:5474 , HOH B:5732
BINDING SITE FOR RESIDUE FAD B 4005
14
BC5
SOFTWARE
ASN B:768 , GLU B:802 , LEU B:873 , SER B:876 , ARG B:880 , PHE B:914 , PHE B:1009 , LEU B:1014 , PRO B:1076 , ALA B:1078 , ALA B:1079 , GLU B:1261 , MOS B:4004 , HOH B:5486 , HOH B:5497
BINDING SITE FOR RESIDUE FYX B 4006
15
BC6
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 ACY A 3007
16
BC7
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 ACY B 4007
17
BC8
SOFTWARE
GLY A:664 , HIS A:665 , ILE A:666 , ARG A:804 , ASN A:869 , SER A:906 , SER A:907 , HOH A:5069 , HOH A:5801
BINDING SITE FOR RESIDUE GOL A 5001
18
BC9
SOFTWARE
GLY B:664 , HIS B:665 , ILE B:666 , ARG B:804 , ASN B:869 , SER B:906 , SER B:907 , HOH B:5048 , HOH B:5889
BINDING SITE FOR RESIDUE GOL B 5002
19
CC1
SOFTWARE
ASP A:594 , ARG A:824 , MET A:826 , HOH A:5160 , HOH A:5646 , HOH A:5885
BINDING SITE FOR RESIDUE GOL A 5003
20
CC2
SOFTWARE
ASP B:594 , PHE B:604 , ARG B:824 , MET B:826 , HOH B:5185 , HOH B:5510
BINDING SITE FOR RESIDUE GOL B 5004
21
CC3
SOFTWARE
GLN A:561 , GLY A:574 , SER A:1184 , SER A:1185 , HOH A:5327 , HOH A:5694
BINDING SITE FOR RESIDUE GOL A 5005
22
CC4
SOFTWARE
GLN B:561 , GLY B:574 , SER B:1184 , SER B:1185 , HOH B:5222 , HOH B:5288
BINDING SITE FOR RESIDUE GOL B 5006
23
CC5
SOFTWARE
GLN A:1088 , TYR A:1091 , TYR A:1254
BINDING SITE FOR RESIDUE GOL A 5007
24
CC6
SOFTWARE
GLN B:1088 , TYR B:1091 , ILE B:1253 , TYR B:1254 , HOH B:5394
BINDING SITE FOR RESIDUE GOL B 5008
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
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
View:
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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.
SCOP Domains
(6, 12)
Info
All SCOP Domains
1a: SCOP_d1v97a1 (A:93-165)
1b: SCOP_d1v97b1 (B:93-165)
2a: SCOP_d1v97a3 (A:537-694)
2b: SCOP_d1v97b3 (B:537-694)
3a: SCOP_d1v97a2 (A:3-92)
3b: SCOP_d1v97b2 (B:3-92)
4a: SCOP_d1v97a4 (A:415-528)
4b: SCOP_d1v97b4 (B:415-528)
5a: SCOP_d1v97a6 (A:192-414)
5b: SCOP_d1v97b6 (B:192-414)
6a: SCOP_d1v97a5 (A:695-1332)
6b: SCOP_d1v97b5 (B:695-1332)
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1v97a1
A:93-165
1b
d1v97b1
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
d1v97a3
A:537-694
2b
d1v97b3
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
d1v97a2
A:3-92
3b
d1v97b2
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
d1v97a4
A:415-528
4b
d1v97b4
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
d1v97a6
A:192-414
5b
d1v97b6
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
d1v97a5
A:695-1332
6b
d1v97b5
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
(6, 12)
Info
all PFAM domains
1a: PFAM_FAD_binding_5_1v97B01 (B:232-412)
1b: PFAM_FAD_binding_5_1v97B02 (B:232-412)
2a: PFAM_Fer2_1v97B03 (B:8-78)
2b: PFAM_Fer2_1v97B04 (B:8-78)
3a: PFAM_Fer2_2_1v97B05 (B:87-162)
3b: PFAM_Fer2_2_1v97B06 (B:87-162)
4a: PFAM_Ald_Xan_dh_C2_1v97B07 (B:701-1236)
4b: PFAM_Ald_Xan_dh_C2_1v97B08 (B:701-1236)
5a: PFAM_Ald_Xan_dh_C_1v97B09 (B:587-693)
5b: PFAM_Ald_Xan_dh_C_1v97B10 (B:587-693)
6a: PFAM_CO_deh_flav_C_1v97B11 (B:419-523)
6b: PFAM_CO_deh_flav_C_1v97B12 (B:419-523)
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Clans
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Families
(
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(
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Organisms
(
)
(
)
Clan
:
FAD_PCMH
(53)
Family
:
FAD_binding_5
(22)
Bos taurus (Bovine)
(7)
1a
FAD_binding_5-1v97B01
B:232-412
1b
FAD_binding_5-1v97B02
B:232-412
Clan
:
Fer2
(69)
Family
:
Fer2
(60)
Bos taurus (Bovine)
(10)
2a
Fer2-1v97B03
B:8-78
2b
Fer2-1v97B04
B:8-78
Family
:
Fer2_2
(24)
Bos taurus (Bovine)
(7)
3a
Fer2_2-1v97B05
B:87-162
3b
Fer2_2-1v97B06
B:87-162
Clan
:
no clan defined [family: Ald_Xan_dh_C2]
(24)
Family
:
Ald_Xan_dh_C2
(24)
Bos taurus (Bovine)
(7)
4a
Ald_Xan_dh_C2-1v97B07
B:701-1236
4b
Ald_Xan_dh_C2-1v97B08
B:701-1236
Clan
:
no clan defined [family: Ald_Xan_dh_C]
(24)
Family
:
Ald_Xan_dh_C
(24)
Bos taurus (Bovine)
(7)
5a
Ald_Xan_dh_C-1v97B09
B:587-693
5b
Ald_Xan_dh_C-1v97B10
B:587-693
Clan
:
no clan defined [family: CO_deh_flav_C]
(22)
Family
:
CO_deh_flav_C
(22)
Bos taurus (Bovine)
(7)
6a
CO_deh_flav_C-1v97B11
B:419-523
6b
CO_deh_flav_C-1v97B12
B:419-523
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