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3UNI
Asym. Unit
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Asym.Unit (443 KB)
Biol.Unit 1 (434 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE MILK XANTHINE DEHYDROGENASE WITH NADH BOUND
Authors
:
B. T. Eger, K. Okamoto, T. Nishino, E. F. Pai
Date
:
15 Nov 11 (Deposition) - 09 May 12 (Release) - 09 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Xanthine Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ishikita, B. T. Eger, K. Okamoto, T. Nishino, E. F. Pai
Protein Conformational Gating Of Enzymatic Activity In Xanthine Oxidoreductase.
J. Am. Chem. Soc. V. 134 999 2012
[
close entry info
]
Hetero Components
(9, 27)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: CARBONATE ION (CO3a)
2b: CARBONATE ION (CO3b)
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: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
5f: GLYCEROL (GOLf)
5g: GLYCEROL (GOLg)
5h: GLYCEROL (GOLh)
5i: GLYCEROL (GOLi)
6a: DIOXOTHIOMOLYBDENUM(VI) ION (MOSa)
6b: DIOXOTHIOMOLYBDENUM(VI) ION (MOSb)
7a: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEa)
7b: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-D... (MTEb)
8a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
8b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
9a: 2-HYDROXYBENZOIC ACID (SALa)
9b: 2-HYDROXYBENZOIC ACID (SALb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CO3
2
Ligand/Ion
CARBONATE ION
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
GOL
9
Ligand/Ion
GLYCEROL
6
MOS
2
Ligand/Ion
DIOXOTHIOMOLYBDENUM(VI) ION
7
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
8
NAI
2
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
9
SAL
2
Ligand/Ion
2-HYDROXYBENZOIC ACID
[
close Hetero Component info
]
Sites
(27, 27)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (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 1333
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 1334
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 , ALA A:1078 , ALA A:1079 , SER A:1080 , VAL A:1081 , SER A:1082 , GLN A:1194 , GLU A:1261 , MOS A:1336 , HOH A:1428 , HOH A:1429 , HOH A:1431
BINDING SITE FOR RESIDUE MTE A 1335
04
AC4
SOFTWARE
GLN A:767 , GLY A:799 , GLU A:802 , PHE A:911 , ARG A:912 , ALA A:1078 , ALA A:1079 , GLU A:1261 , MTE A:1335 , SAL A:1344 , HOH A:1440
BINDING SITE FOR RESIDUE MOS A 1336
05
AC5
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 , NAI A:1338 , HOH A:1560 , HOH A:1856 , HOH A:1895
BINDING SITE FOR RESIDUE FAD A 1337
06
AC6
SOFTWARE
GLU A:263 , LYS A:271 , SER A:356 , PRO A:357 , ILE A:358 , TYR A:393 , ARG A:394 , ASP A:429 , ASP A:430 , ILE A:431 , GLY A:458 , ALA A:460 , ASP A:461 , PRO A:501 , GLY A:502 , ARG A:508 , SER A:1225 , FAD A:1337 , HOH A:1546 , HOH A:1547 , HOH A:1751 , HOH A:1856
BINDING SITE FOR RESIDUE NAI A 1338
07
AC7
SOFTWARE
TRP A:336 , LYS A:422 , GLN A:423 , PHE A:549 , ASP A:1170
BINDING SITE FOR RESIDUE GOL A 1339
08
AC8
SOFTWARE
LEU A:580 , ALA A:581 , ARG A:793 , TYR A:1062 , ILE A:1063 , HOH A:1509 , HOH A:1771 , HOH B:1768
BINDING SITE FOR RESIDUE GOL A 1340
09
AC9
SOFTWARE
HIS A:665 , ILE A:666 , ARG A:804 , ILE A:835 , ASN A:869 , SER A:907 , HOH A:1579
BINDING SITE FOR RESIDUE GOL A 1341
10
BC1
SOFTWARE
ASP A:594 , PHE A:604 , CYS A:825 , MET A:826 , HOH A:1717
BINDING SITE FOR RESIDUE GOL A 1342
11
BC2
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 CO3 A 1343
12
BC3
SOFTWARE
GLU A:802 , ARG A:880 , PHE A:914 , SER A:1008 , PHE A:1009 , THR A:1010 , VAL A:1011 , LEU A:1014 , MOS A:1336 , HOH A:1439 , HOH A:1440
BINDING SITE FOR RESIDUE SAL A 1344
13
BC4
SOFTWARE
ALA A:867 , SER A:870 , ARG A:871 , ASP A:872 , SER A:874 , SER A:907 , ASN A:908
BINDING SITE FOR RESIDUE CA A 1345
14
BC5
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 1333
15
BC6
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 1334
16
BC7
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 , ALA B:1078 , ALA B:1079 , SER B:1080 , VAL B:1081 , SER B:1082 , GLN B:1194 , GLU B:1261 , MOS B:1336 , HOH B:1441 , HOH B:1442 , HOH B:1443
BINDING SITE FOR RESIDUE MTE B 1335
17
BC8
SOFTWARE
GLN B:767 , PHE B:798 , GLY B:799 , GLU B:802 , PHE B:911 , ARG B:912 , ALA B:1078 , ALA B:1079 , GLU B:1261 , MTE B:1335 , SAL B:1345 , HOH B:1552
BINDING SITE FOR RESIDUE MOS B 1336
18
BC9
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 , ILE B:403 , LEU B:404 , LYS B:422 , ASP B:429 , NAI B:1338 , HOH B:1733 , HOH B:1734 , HOH B:1738 , HOH B:1787 , HOH B:1800
BINDING SITE FOR RESIDUE FAD B 1337
19
CC1
SOFTWARE
GLU B:263 , SER B:356 , PRO B:357 , ILE B:358 , TYR B:393 , ARG B:394 , ASP B:429 , ASP B:430 , ILE B:431 , GLY B:458 , ALA B:460 , ASP B:461 , PRO B:501 , ARG B:508 , SER B:1225 , FAD B:1337 , HOH B:1595 , HOH B:1738 , HOH B:1742 , HOH B:1784 , HOH B:1785
BINDING SITE FOR RESIDUE NAI B 1338
20
CC2
SOFTWARE
HOH A:1631 , LEU B:580 , ALA B:581 , ARG B:793 , TYR B:1062 , ILE B:1063 , HOH B:1416 , HOH B:1421
BINDING SITE FOR RESIDUE GOL B 1339
21
CC3
SOFTWARE
ASP B:594 , PHE B:604 , PRO B:675 , CYS B:825 , MET B:826 , HOH B:1725
BINDING SITE FOR RESIDUE GOL B 1340
22
CC4
SOFTWARE
CYS B:662 , HIS B:665 , ILE B:666 , ARG B:804 , ILE B:835 , ASN B:869 , SER B:906 , SER B:907
BINDING SITE FOR RESIDUE GOL B 1341
23
CC5
SOFTWARE
ARG B:427 , PHE B:549 , LYS B:994 , GLU B:1163 , ASP B:1170 , HIS B:1171 , LYS B:1172
BINDING SITE FOR RESIDUE GOL B 1342
24
CC6
SOFTWARE
GLN B:561 , GLY B:574 , SER B:1184 , SER B:1185 , PRO B:1188 , HOH B:1399
BINDING SITE FOR RESIDUE GOL B 1343
25
CC7
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 CO3 B 1344
26
CC8
SOFTWARE
GLU B:802 , ARG B:880 , PHE B:914 , PHE B:1009 , THR B:1010 , LEU B:1014 , MOS B:1336 , HOH B:1552
BINDING SITE FOR RESIDUE SAL B 1345
27
CC9
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 1346
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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
[
close PROSITE info
]
Exons
(0, 0)
Info
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SCOP Domains
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CATH Domains
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Pfam Domains
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