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3B9J
Asym. Unit
Info
Asym.Unit (409 KB)
Biol.Unit 1 (203 KB)
Biol.Unit 2 (203 KB)
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(1)
Title
:
STRUCTURE OF XANTHINE OXIDASE WITH 2-HYDROXY-6-METHYLPURINE
Authors
:
J. M. Pauff, J. Zhang, C. E. Bell, R. Hille
Date
:
05 Nov 07 (Deposition) - 04 Dec 07 (Release) - 14 Apr 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,I,J,K
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: I,J,K (1x)
Keywords
:
Oxidoreductase, Catalysis, Intermediate, Substrate Orientation, Peroxisome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Pauff, J. Zhang, C. E. Bell, R. Hille
Substrate Orientation In Xanthine Oxidase: Crystal Structure Of Enzyme In Reaction With 2-Hydroxy-6-Methylpurine.
J. Biol. Chem. V. 283 4818 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 13)
Info
All Hetero Components
1a: 6-METHYL-3,9-DIHYDRO-2H-PURIN-2-ON... (290a)
1b: 6-METHYL-3,9-DIHYDRO-2H-PURIN-2-ON... (290b)
2a: CALCIUM ION (CAa)
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: DIOXOTHIOMOLYBDENUM(VI) ION (MOSa)
5b: DIOXOTHIOMOLYBDENUM(VI) ION (MOSb)
6a: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEa)
6b: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
290
2
Ligand/Ion
6-METHYL-3,9-DIHYDRO-2H-PURIN-2-ONE
2
CA
1
Ligand/Ion
CALCIUM ION
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
MOS
2
Ligand/Ion
DIOXOTHIOMOLYBDENUM(VI) ION
6
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
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE C:877 , THR C:909 , GLN C:918
BINDING SITE FOR RESIDUE CA C 1
02
AC2
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 601
03
AC3
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 , CYS A:73
BINDING SITE FOR RESIDUE FES A 602
04
AC4
SOFTWARE
GLN A:112 , CYS A:150 , GLY C:796 , GLY C:797 , PHE C:798 , ARG C:912 , MET C:1038 , GLY C:1039 , GLN C:1040 , ALA C:1079 , SER C:1080 , VAL C:1081 , SER C:1082 , GLN C:1194 , MOS C:1334 , HOH C:1552
BINDING SITE FOR RESIDUE MTE C 1333
05
AC5
SOFTWARE
GLN C:767 , GLY C:799 , GLU C:802 , ALA C:910 , PHE C:911 , ARG C:912 , ALA C:1078 , ALA C:1079 , GLU C:1261 , MTE C:1333 , 290 C:1335
BINDING SITE FOR RESIDUE MOS C 1334
06
AC6
SOFTWARE
GLU A:45 , GLY A: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 , ASP B:360 , LEU B:404 , HOH B:618 , HOH B:620 , HOH B:649 , HOH B:665 , HOH B:673
BINDING SITE FOR RESIDUE FAD B 606
07
AC7
SOFTWARE
GLN I:112 , CYS I:113 , GLY I:114 , CYS I:116 , CYS I:148 , ARG I:149 , CYS I:150
BINDING SITE FOR RESIDUE FES I 601
08
AC8
SOFTWARE
GLY I:42 , CYS I:43 , GLY I:44 , GLY I:46 , GLY I:47 , CYS I:48 , GLY I:49 , CYS I:51 , CYS I:73
BINDING SITE FOR RESIDUE FES I 602
09
AC9
SOFTWARE
GLN I:112 , CYS I:150 , GLY K:797 , PHE K:798 , GLY K:799 , ARG K:912 , MET K:1038 , GLY K:1039 , GLN K:1040 , ALA K:1079 , SER K:1080 , VAL K:1081 , SER K:1082 , GLN K:1194 , GLU K:1261 , MOS K:1334 , HOH K:1419 , HOH K:1453 , HOH K:1615
BINDING SITE FOR RESIDUE MTE K 1333
10
BC1
SOFTWARE
GLN K:767 , PHE K:798 , GLY K:799 , GLU K:802 , PHE K:911 , ARG K:912 , ALA K:1078 , ALA K:1079 , GLU K:1261 , MTE K:1333 , 290 K:1335
BINDING SITE FOR RESIDUE MOS K 1334
11
BC2
SOFTWARE
GLU I:45 , GLY I:46 , LYS J:256 , LEU J:257 , VAL J:258 , VAL J:259 , GLY J:260 , ASN J:261 , THR J:262 , GLU J:263 , ILE J:264 , PHE J:337 , VAL J:342 , ALA J:346 , SER J:347 , GLY J:350 , ASN J:351 , ILE J:353 , THR J:354 , SER J:359 , ASP J:360 , LEU J:404 , HOH J:629 , HOH J:645 , HOH J:660
BINDING SITE FOR RESIDUE FAD J 606
12
BC3
SOFTWARE
GLU C:802 , ARG C:880 , PHE C:914 , PHE C:1009 , THR C:1010 , ALA C:1078 , ALA C:1079 , GLU C:1261 , MOS C:1334 , HOH C:1365 , HOH C:1495
BINDING SITE FOR RESIDUE 290 C 1335
13
BC4
SOFTWARE
GLU K:802 , ARG K:880 , PHE K:914 , SER K:1008 , PHE K:1009 , THR K:1010 , ALA K:1078 , ALA K:1079 , GLU K:1261 , MOS K:1334 , HOH K:1624 , HOH K:1625
BINDING SITE FOR RESIDUE 290 K 1335
[
close Site info
]
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,I:4-91)
2: 2FE2S_FER_1 (A:43-51,I:43-51)
3: FAD_PCMH (B:229-414,J:229-414)
4: MOLYBDOPTERIN_EUK (C:797-832,K: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
I:4-91
2
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
XDH_BOVIN
43-51
2
A:43-51
I:43-51
3
FAD_PCMH
PS51387
PCMH-type FAD-binding domain profile.
XDH_BOVIN
229-414
2
B:229-414
J:229-414
4
MOLYBDOPTERIN_EUK
PS00559
Eukaryotic molybdopterin oxidoreductases signature.
XDH_BOVIN
797-832
2
C:797-832
K: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_d3b9ja1 (A:93-164)
1b: SCOP_d3b9ji1 (I:93-164)
2a: SCOP_d3b9jc1 (C:571-694)
2b: SCOP_d3b9jk1 (K:571-694)
3a: SCOP_d3b9ja2 (A:3-92)
3b: SCOP_d3b9ji2 (I:3-92)
4a: SCOP_d3b9jb1 (B:415-528)
4b: SCOP_d3b9jj1 (J:415-528)
5a: SCOP_d3b9jb2 (B:224-414)
5b: SCOP_d3b9jj2 (J:224-414)
6a: SCOP_d3b9jc2 (C:695-1328)
6b: SCOP_d3b9jk2 (K:695-1320)
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Classes
(
)
(
)
Folds
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)
(
)
Superfamilies
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)
(
)
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
d3b9ja1
A:93-164
1b
d3b9ji1
I:93-164
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
d3b9jc1
C:571-694
2b
d3b9jk1
K:571-694
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
d3b9ja2
A:3-92
3b
d3b9ji2
I:3-92
Fold
:
CO dehydrogenase flavoprotein C-domain-like
(111)
Superfamily
:
CO dehydrogenase flavoprotein C-terminal domain-like
(35)
Family
:
automated matches
(12)
Protein domain
:
automated matches
(12)
Cow (Bos taurus) [TaxId: 9913]
(10)
4a
d3b9jb1
B:415-528
4b
d3b9jj1
J: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
:
automated matches
(10)
Cow (Bos taurus) [TaxId: 9913]
(10)
5a
d3b9jb2
B:224-414
5b
d3b9jj2
J:224-414
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
d3b9jc2
C:695-1328
6b
d3b9jk2
K:695-1320
[
close SCOP info
]
CATH Domains
(5, 10)
Info
all CATH domains
1a: CATH_3b9jB03 (B:413-528)
1b: CATH_3b9jJ03 (J:413-528)
2a: CATH_3b9jB01 (B:224-286)
2b: CATH_3b9jJ01 (J:224-286)
3a: CATH_3b9jB02 (B:287-412)
3b: CATH_3b9jJ02 (J:287-412)
4a: CATH_3b9jA01 (A:3-87)
4b: CATH_3b9jI01 (I:3-87)
5a: CATH_3b9jA02 (A:92-164)
5b: CATH_3b9jI02 (I:92-164)
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)
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)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
[code=3.30.390.50, no name defined]
(22)
Cattle (Bos taurus)
(2)
1a
3b9jB03
B:413-528
1b
3b9jJ03
J:413-528
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
(50)
Homologous Superfamily
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
(50)
Cattle (Bos taurus)
(2)
2a
3b9jB01
B:224-286
2b
3b9jJ01
J:224-286
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
(63)
Homologous Superfamily
:
[code=3.30.465.10, no name defined]
(63)
Cattle (Bos taurus)
(2)
3a
3b9jB02
B:287-412
3b
3b9jJ02
J:287-412
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Cattle (Bos taurus)
(6)
4a
3b9jA01
A:3-87
4b
3b9jI01
I:3-87
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.120, no name defined]
(29)
Cattle (Bos taurus)
(2)
5a
3b9jA02
A:92-164
5b
3b9jI02
I:92-164
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (409 KB)
Header - Asym.Unit
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