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3ETR
Asym. Unit
Info
Asym.Unit (417 KB)
Biol.Unit 1 (408 KB)
Biol.Unit 2 (209 KB)
Biol.Unit 3 (208 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF XANTHINE OXIDASE IN COMPLEX WITH LUMAZINE
Authors
:
J. M. Pauff, H. Cao, R. Hille
Date
:
08 Oct 08 (Deposition) - 27 Jan 09 (Release) - 10 Sep 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,L,M,N
Biol. Unit 1: A,B,C,L,M,N (1x)
Biol. Unit 2: A,B,C (1x)
Biol. Unit 3: L,M,N (1x)
Keywords
:
Protein-Ligand Complex, Enzyme Catalysis, Substrate Orientation, Fad, Flavoprotein, Iron, Iron-Sulfur, Metal-Binding, Molybdenum, Nad, Oxidoreductase, Peroxisome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Pauff, H. Cao, R. Hille
Substrate Orientation And Catalysis At The Molybdenum Site In Xanthine Oxidase: Crystal Structures In Complex With Xanthine And Lumazine.
J. Biol. Chem. V. 284 8760 2009
[
close entry info
]
Hetero Components
(6, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
4a: PTERIDINE-2,4(1H,3H)-DIONE (LUZa)
4b: PTERIDINE-2,4(1H,3H)-DIONE (LUZb)
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
CA
1
Ligand/Ion
CALCIUM ION
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
LUZ
2
Ligand/Ion
PTERIDINE-2,4(1H,3H)-DIONE
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
[
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]
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
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
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 602
03
AC3
SOFTWARE
GLY A:46 , 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 , HOH B:641 , HOH B:647 , HOH B:652 , HOH B:658 , HOH B:745 , HOH B:755 , HOH B:756
BINDING SITE FOR RESIDUE FAD B 606
04
AC4
SOFTWARE
GLN A:112 , CYS A:150 , GLY C:796 , GLY C:797 , PHE C:798 , GLY C:799 , ARG C:912 , MET C:1038 , GLY C:1039 , GLN C:1040 , SER C:1080 , VAL C:1081 , SER C:1082 , GLN C:1194 , MOS C:1327 , HOH C:1391 , HOH C:1420 , HOH C:1473
BINDING SITE FOR RESIDUE MTE C1326
05
AC5
SOFTWARE
GLN C:767 , GLY C:799 , THR C:1077 , ALA C:1078 , ALA C:1079 , GLU C:1261 , MTE C:1326
BINDING SITE FOR RESIDUE MOS C1327
06
AC6
SOFTWARE
GLU C:802 , LEU C:873 , PHE C:914 , PHE C:1009 , THR C:1010 , VAL C:1011 , LEU C:1014 , ALA C:1079
BINDING SITE FOR RESIDUE LUZ C 1
07
AC7
SOFTWARE
HIS C:840 , THR C:909 , GLN C:918 , HOH C:1660
BINDING SITE FOR RESIDUE CA C1328
08
AC8
SOFTWARE
GLN L:112 , CYS L:113 , GLY L:114 , CYS L:116 , CYS L:148 , ARG L:149 , CYS L:150
BINDING SITE FOR RESIDUE FES L 601
09
AC9
SOFTWARE
GLY L:42 , CYS L:43 , GLY L:44 , GLY L:46 , GLY L:47 , CYS L:48 , GLY L:49 , CYS L:51 , CYS L:73
BINDING SITE FOR RESIDUE FES L 602
10
BC1
SOFTWARE
GLU L:45 , GLY L:46 , LYS M:256 , LEU M:257 , VAL M:258 , VAL M:259 , GLY M:260 , ASN M:261 , THR M:262 , GLU M:263 , ILE M:264 , ALA M:301 , PHE M:337 , ALA M:338 , ALA M:346 , SER M:347 , GLY M:350 , ASN M:351 , THR M:354 , SER M:359 , ASP M:360 , ILE M:403 , LEU M:404 , HOH M:626 , HOH M:629 , HOH M:665 , HOH M:688 , HOH M:700
BINDING SITE FOR RESIDUE FAD M 606
11
BC2
SOFTWARE
GLN L:112 , CYS L:150 , GLY N:796 , GLY N:797 , PHE N:798 , ARG N:912 , MET N:1038 , GLY N:1039 , GLN N:1040 , SER N:1080 , VAL N:1081 , SER N:1082 , GLN N:1194 , GLU N:1261 , MOS N:1327 , HOH N:1415 , HOH N:1516
BINDING SITE FOR RESIDUE MTE N1326
12
BC3
SOFTWARE
LUZ N:1 , GLN N:767 , GLY N:799 , GLU N:802 , ALA N:910 , PHE N:911 , ARG N:912 , ALA N:1078 , ALA N:1079 , GLU N:1261 , MTE N:1326
BINDING SITE FOR RESIDUE MOS N1327
13
BC4
SOFTWARE
GLU N:802 , ARG N:880 , PHE N:914 , PHE N:1009 , THR N:1010 , LEU N:1014 , ALA N:1078 , ALA N:1079 , MOS N:1327
BINDING SITE FOR RESIDUE LUZ N 1
[
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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,L:4-91)
2: 2FE2S_FER_1 (A:43-51,L:43-51)
3: FAD_PCMH (B:229-414,M:229-414)
4: MOLYBDOPTERIN_EUK (C:797-832,N: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
L:4-91
2
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
XDH_BOVIN
43-51
2
A:43-51
L:43-51
3
FAD_PCMH
PS51387
PCMH-type FAD-binding domain profile.
XDH_BOVIN
229-414
2
B:229-414
M:229-414
4
MOLYBDOPTERIN_EUK
PS00559
Eukaryotic molybdopterin oxidoreductases signature.
XDH_BOVIN
797-832
2
C:797-832
N: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_d3etra2 (A:93-165)
1b: SCOP_d3etrl2 (L:93-165)
2a: SCOP_d3etrc1 (C:571-694)
2b: SCOP_d3etrn1 (N:571-694)
3a: SCOP_d3etra1 (A:2-92)
3b: SCOP_d3etrl1 (L:2-92)
4a: SCOP_d3etrb2 (B:415-528)
4b: SCOP_d3etrm2 (M:415-528)
5a: SCOP_d3etrb1 (B:224-414)
5b: SCOP_d3etrm1 (M:224-414)
6a: SCOP_d3etrc2 (C:695-1325)
6b: SCOP_d3etrn2 (N:695-1315)
View:
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Classes
(
)
(
)
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
:
automated matches
(9)
Cow (Bos taurus) [TaxId: 9913]
(9)
1a
d3etra2
A:93-165
1b
d3etrl2
L:93-165
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
CO dehydrogenase molybdoprotein N-domain-like
(44)
Family
:
automated matches
(10)
Protein domain
:
automated matches
(10)
Cow (Bos taurus) [TaxId: 9913]
(9)
2a
d3etrc1
C:571-694
2b
d3etrn1
N: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
:
automated matches
(14)
Cow (Bos taurus) [TaxId: 9913]
(9)
3a
d3etra1
A:2-92
3b
d3etrl1
L:2-92
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
d3etrb2
B:415-528
4b
d3etrm2
M: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
d3etrb1
B:224-414
5b
d3etrm1
M:224-414
Fold
:
Molybdenum cofactor-binding domain
(44)
Superfamily
:
Molybdenum cofactor-binding domain
(44)
Family
:
Molybdenum cofactor-binding domain
(44)
Protein domain
:
automated matches
(10)
Cow (Bos taurus) [TaxId: 9913]
(9)
6a
d3etrc2
C:695-1325
6b
d3etrn2
N:695-1315
[
close SCOP info
]
CATH Domains
(5, 10)
Info
all CATH domains
1a: CATH_3etrB03 (B:413-528)
1b: CATH_3etrM03 (M:413-528)
2a: CATH_3etrB01 (B:224-286)
2b: CATH_3etrM01 (M:224-286)
3a: CATH_3etrB02 (B:287-412)
3b: CATH_3etrM02 (M:287-412)
4a: CATH_3etrA01 (A:3-87)
4b: CATH_3etrL01 (L:3-87)
5a: CATH_3etrA02 (A:92-165)
5b: CATH_3etrL02 (L:92-165)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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)
Bovine (Bos taurus)
(2)
1a
3etrB03
B:413-528
1b
3etrM03
M:413-528
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
(50)
Homologous Superfamily
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
(50)
Bovine (Bos taurus)
(2)
2a
3etrB01
B:224-286
2b
3etrM01
M:224-286
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
(63)
Homologous Superfamily
:
[code=3.30.465.10, no name defined]
(63)
Bovine (Bos taurus)
(2)
3a
3etrB02
B:287-412
3b
3etrM02
M:287-412
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Bovine (Bos taurus)
(4)
4a
3etrA01
A:3-87
4b
3etrL01
L: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)
Bovine (Bos taurus)
(2)
5a
3etrA02
A:92-165
5b
3etrL02
L:92-165
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (417 KB)
Header - Asym.Unit
Biol.Unit 1 (408 KB)
Header - Biol.Unit 1
Biol.Unit 2 (209 KB)
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Biol.Unit 3 (208 KB)
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