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1N5X
Asym. Unit
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Asym.Unit (358 KB)
Biol.Unit 1 (351 KB)
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(1)
Title
:
XANTHINE DEHYDROGENASE FROM BOVINE MILK WITH INHIBITOR TEI-6720 BOUND
Authors
:
K. Okamoto, B. T. Eger, T. Nishino, S. Kondo, E. F. Pai, T. Nishino
Date
:
07 Nov 02 (Deposition) - 18 Mar 03 (Release) - 08 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase, Molybdopterin, Tei-6720, Flavoprotein, Fad, Iron- Sulfur Center, Fe2/S2 Center
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Okamoto, B. T. Eger, T. Nishino, S. Kondo, E. F. Pai, T. Nishino
An Extremely Potent Inhibitor Of Xanthine Oxidoreductase: Crystal Structure Of The Enzyme-Inhibitor Complex And Mechanism Of Inhibition
J. Biol. Chem. V. 278 1848 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 12)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2b: FE2/S2 (INORGANIC) CLUSTER (FESb)
2c: FE2/S2 (INORGANIC) CLUSTER (FESc)
2d: FE2/S2 (INORGANIC) CLUSTER (FESd)
3a: DIOXOTHIOMOLYBDENUM(VI) ION (MOSa)
3b: DIOXOTHIOMOLYBDENUM(VI) ION (MOSb)
4a: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEa)
4b: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEb)
5a: 2-(3-CYANO-4-ISOBUTOXY-PHENYL)-4-M... (TEIa)
5b: 2-(3-CYANO-4-ISOBUTOXY-PHENYL)-4-M... (TEIb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
3
MOS
2
Ligand/Ion
DIOXOTHIOMOLYBDENUM(VI) ION
4
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
5
TEI
2
Ligand/Ion
2-(3-CYANO-4-ISOBUTOXY-PHENYL)-4-METHYL-5-THIAZOLE-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(12, 12)
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)
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 , LEU A:744
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
GLN A:112 , CYS A:150 , GLY A:796 , GLY A:797 , PHE A:798 , ARG A:912 , MET A:1038 , GLY A:1039 , GLN A:1040 , THR A:1077 , ALA A:1079 , SER A:1080 , VAL A:1081 , SER A:1082 , THR A:1083 , GLN A:1194 , GLU A:1261 , MOS A:3004
BINDING SITE FOR RESIDUE MTE A 3003
04
AC4
SOFTWARE
GLN A:767 , GLY A:799 , GLU A:802 , ARG A:912 , ALA A:1078 , ALA A:1079 , GLU A:1261 , MTE A:3003 , TEI A:3006
BINDING SITE FOR RESIDUE MOS A 3004
05
AC5
SOFTWARE
GLU A:45 , GLY A:46 , LEU A:74 , 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 , THR A:354 , SER A:359 , ASP A:360 , LEU A:404 , LYS A:422 , ASP A:429
BINDING SITE FOR RESIDUE FAD A 3005
06
AC6
SOFTWARE
LEU A:648 , ASN A:768 , LYS A:771 , GLU A:802 , LEU A:873 , SER A:876 , ARG A:880 , PHE A:914 , PHE A:1009 , THR A:1010 , VAL A:1011 , LEU A:1014 , MOS A:3004
BINDING SITE FOR RESIDUE TEI A 3006
07
AC7
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
08
AC8
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
09
AC9
SOFTWARE
GLN B:112 , CYS B:150 , GLY B:796 , GLY B:797 , PHE B:798 , ARG B:912 , MET B:1038 , GLY B:1039 , GLN B:1040 , THR B:1077 , ALA B:1079 , SER B:1080 , VAL B:1081 , SER B:1082 , THR B:1083 , GLN B:1194 , GLU B:1261 , MOS B:4004
BINDING SITE FOR RESIDUE MTE B 4003
10
BC1
SOFTWARE
GLN B:767 , GLY B:799 , GLU B:802 , ARG B:912 , ALA B:1078 , ALA B:1079 , GLU B:1261 , MTE B:4003 , TEI B:4006
BINDING SITE FOR RESIDUE MOS B 4004
11
BC2
SOFTWARE
GLU B:45 , GLY B:46 , LEU B:74 , 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 , THR B:354 , SER B:359 , ASP B:360 , LEU B:404 , LYS B:422 , ASP B:429
BINDING SITE FOR RESIDUE FAD B 4005
12
BC3
SOFTWARE
LEU B:648 , ASN B:768 , LYS B:771 , GLU B:802 , LEU B:873 , SER B:876 , ARG B:880 , PHE B:914 , PHE B:1009 , THR B:1010 , VAL B:1011 , LEU B:1014 , MOS B:4004
BINDING SITE FOR RESIDUE TEI B 4006
[
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
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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_d1n5xa1 (A:93-165)
1b: SCOP_d1n5xb1 (B:93-165)
2a: SCOP_d1n5xa3 (A:537-694)
2b: SCOP_d1n5xb3 (B:537-694)
3a: SCOP_d1n5xa2 (A:3-92)
3b: SCOP_d1n5xb2 (B:3-92)
4a: SCOP_d1n5xa4 (A:415-531)
4b: SCOP_d1n5xb4 (B:415-531)
5a: SCOP_d1n5xa6 (A:192-414)
5b: SCOP_d1n5xb6 (B:192-414)
6a: SCOP_d1n5xa5 (A:695-1332)
6b: SCOP_d1n5xb5 (B:695-1332)
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
:
Xanthine oxidase, domain 2
(11)
Cow (Bos taurus) [TaxId: 9913]
(11)
1a
d1n5xa1
A:93-165
1b
d1n5xb1
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
d1n5xa3
A:537-694
2b
d1n5xb3
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
d1n5xa2
A:3-92
3b
d1n5xb2
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
d1n5xa4
A:415-531
4b
d1n5xb4
B:415-531
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
d1n5xa6
A:192-414
5b
d1n5xb6
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
d1n5xa5
A:695-1332
6b
d1n5xb5
B:695-1332
[
close SCOP info
]
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_1n5xB01 (B:232-412)
1b: PFAM_FAD_binding_5_1n5xB02 (B:232-412)
2a: PFAM_Fer2_1n5xB03 (B:8-78)
2b: PFAM_Fer2_1n5xB04 (B:8-78)
3a: PFAM_Fer2_2_1n5xB05 (B:87-162)
3b: PFAM_Fer2_2_1n5xB06 (B:87-162)
4a: PFAM_Ald_Xan_dh_C2_1n5xB07 (B:701-1236)
4b: PFAM_Ald_Xan_dh_C2_1n5xB08 (B:701-1236)
5a: PFAM_Ald_Xan_dh_C_1n5xB09 (B:587-693)
5b: PFAM_Ald_Xan_dh_C_1n5xB10 (B:587-693)
6a: PFAM_CO_deh_flav_C_1n5xB11 (B:419-523)
6b: PFAM_CO_deh_flav_C_1n5xB12 (B:419-523)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_PCMH
(53)
Family
:
FAD_binding_5
(22)
Bos taurus (Bovine)
(7)
1a
FAD_binding_5-1n5xB01
B:232-412
1b
FAD_binding_5-1n5xB02
B:232-412
Clan
:
Fer2
(69)
Family
:
Fer2
(60)
Bos taurus (Bovine)
(10)
2a
Fer2-1n5xB03
B:8-78
2b
Fer2-1n5xB04
B:8-78
Family
:
Fer2_2
(24)
Bos taurus (Bovine)
(7)
3a
Fer2_2-1n5xB05
B:87-162
3b
Fer2_2-1n5xB06
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_C2-1n5xB07
B:701-1236
4b
Ald_Xan_dh_C2-1n5xB08
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-1n5xB09
B:587-693
5b
Ald_Xan_dh_C-1n5xB10
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-1n5xB11
B:419-523
6b
CO_deh_flav_C-1n5xB12
B:419-523
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Asym.Unit (358 KB)
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