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1GTE
Biol. Unit 1
Info
Asym.Unit (736 KB)
Biol.Unit 1 (365 KB)
Biol.Unit 2 (372 KB)
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(1)
Title
:
DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, BINARY COMPLEX WITH 5-IODOURACIL
Authors
:
D. Dobritzsch, S. Ricagno, G. Schneider, K. D. Schnackerz, Y. Lindqvist
Date
:
15 Jan 02 (Deposition) - 11 Apr 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Electron Transfer, Flavin, Iron-Sulfur Clusters, Pyrimidine Catabolism, 5-Fluorouracil Degradation, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Dobritzsch, S. Ricagno, G. Schneider, K. D. Schnackerz, Y. Lindqvist
Crystal Structure Of The Productive Ternary Complex Of Dihydropyrimidine Dehydrogenase With Nadph And 5-Iodouracil. Implications For Mechanism Of Inhibition And Electron Transfer
J. Biol. Chem. V. 277 13155 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 14)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2a: FLAVIN MONONUCLEOTIDE (FMNa)
2b: FLAVIN MONONUCLEOTIDE (FMNb)
2c: FLAVIN MONONUCLEOTIDE (FMNc)
2d: FLAVIN MONONUCLEOTIDE (FMNd)
3a: 5-IODOURACIL (IURa)
3b: 5-IODOURACIL (IURb)
3c: 5-IODOURACIL (IURc)
3d: 5-IODOURACIL (IURd)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
4e: IRON/SULFUR CLUSTER (SF4e)
4f: IRON/SULFUR CLUSTER (SF4f)
4g: IRON/SULFUR CLUSTER (SF4g)
4h: IRON/SULFUR CLUSTER (SF4h)
4i: IRON/SULFUR CLUSTER (SF4i)
4j: IRON/SULFUR CLUSTER (SF4j)
4k: IRON/SULFUR CLUSTER (SF4k)
4l: IRON/SULFUR CLUSTER (SF4l)
4m: IRON/SULFUR CLUSTER (SF4m)
4n: IRON/SULFUR CLUSTER (SF4n)
4o: IRON/SULFUR CLUSTER (SF4o)
4p: IRON/SULFUR CLUSTER (SF4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
FMN
2
Ligand/Ion
FLAVIN MONONUCLEOTIDE
3
IUR
2
Ligand/Ion
5-IODOURACIL
4
SF4
8
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:91 , PRO A:92 , ILE A:97 , ASN A:120 , CYS A:130 , THR A:132 , CYS A:136 , GLN A:156
BINDING SITE FOR RESIDUE SF4 A1026
02
AC2
SOFTWARE
CYS A:79 , LEU A:80 , LYS A:81 , CYS A:82 , PRO A:86 , CYS A:87 , CYS A:140 , ASN A:141 , LEU A:142 , ILE A:150 , ILE A:152
BINDING SITE FOR RESIDUE SF4 A1027
03
AC3
SOFTWARE
ILE A:948 , CYS A:953 , ILE A:954 , ASN A:955 , CYS A:956 , GLY A:957 , LYS A:958 , CYS A:959 , CYS A:996 , PRO A:997 , CYS A:1001 , ILE A:1002
BINDING SITE FOR RESIDUE SF4 A1028
04
AC4
SOFTWARE
CYS A:963 , TYR A:968 , ILE A:971 , VAL A:982 , CYS A:986 , THR A:987 , GLY A:988 , CYS A:989 , THR A:990 , CYS A:992 , MET A:1004
BINDING SITE FOR RESIDUE SF4 A1029
05
AC5
SOFTWARE
ALA A:549 , SER A:550 , ALA A:551 , LYS A:574 , THR A:575 , ILE A:590 , ASN A:609 , GLU A:611 , ASN A:668 , LYS A:709 , THR A:735 , ASN A:736 , SER A:766 , GLY A:767 , THR A:793 , GLY A:794 , GLY A:795 , CYS A:816 , SER A:817 , GLN A:820 , IUR A:1034 , HOH A:2823 , HOH A:3162 , HOH A:3163
BINDING SITE FOR RESIDUE FMN A1030
06
AC6
SOFTWARE
VAL A:129 , PRO A:131 , GLY A:194 , GLY A:196 , PRO A:197 , ALA A:198 , GLU A:218 , LYS A:219 , GLN A:220 , GLY A:225 , LEU A:226 , GLU A:230 , ARG A:235 , SER A:260 , LEU A:261 , GLY A:282 , ILE A:283 , GLY A:284 , PRO A:286 , LEU A:310 , THR A:343 , ASP A:346 , GLY A:480 , ASP A:481 , ASN A:487 , THR A:488 , THR A:489 , SER A:492 , HOH A:2376 , HOH A:2670 , HOH A:3164 , HOH A:3165 , HOH A:3166 , HOH A:3167 , HOH A:3168 , HOH A:3169 , HOH A:3170
BINDING SITE FOR RESIDUE FAD A1031
07
AC7
SOFTWARE
ASN A:609 , GLU A:611 , ASN A:668 , SER A:670 , ASN A:736 , THR A:737 , FMN A:1030 , HOH A:2798
BINDING SITE FOR RESIDUE IUR A1034
08
AC8
SOFTWARE
CYS B:91 , PRO B:92 , LEU B:95 , ILE B:97 , ASN B:120 , CYS B:130 , THR B:132 , CYS B:136 , GLN B:156
BINDING SITE FOR RESIDUE SF4 B1026
09
AC9
SOFTWARE
CYS B:79 , LEU B:80 , LYS B:81 , CYS B:82 , PRO B:86 , CYS B:87 , CYS B:140 , ASN B:141 , LEU B:142 , ILE B:150 , ILE B:152
BINDING SITE FOR RESIDUE SF4 B1027
10
BC1
SOFTWARE
ILE B:948 , CYS B:953 , ILE B:954 , CYS B:956 , GLY B:957 , LYS B:958 , CYS B:959 , CYS B:996 , PRO B:997 , ILE B:998 , CYS B:1001 , ILE B:1002
BINDING SITE FOR RESIDUE SF4 B1028
11
BC2
SOFTWARE
CYS B:963 , TYR B:968 , ILE B:971 , VAL B:982 , CYS B:986 , THR B:987 , GLY B:988 , CYS B:989 , THR B:990 , CYS B:992
BINDING SITE FOR RESIDUE SF4 B1029
12
BC3
SOFTWARE
ALA B:549 , SER B:550 , ALA B:551 , LYS B:574 , THR B:575 , ILE B:590 , ASN B:609 , GLU B:611 , ASN B:668 , LYS B:709 , THR B:735 , ASN B:736 , THR B:737 , SER B:766 , GLY B:767 , THR B:793 , GLY B:794 , GLY B:795 , CYS B:816 , SER B:817 , GLN B:820 , IUR B:1034 , HOH B:2857 , HOH B:2973 , HOH B:3211 , HOH B:3212
BINDING SITE FOR RESIDUE FMN B1030
13
BC4
SOFTWARE
VAL B:129 , PRO B:131 , GLY B:194 , GLY B:196 , PRO B:197 , ALA B:198 , GLU B:218 , LYS B:219 , GLN B:220 , GLY B:225 , LEU B:226 , GLU B:230 , ARG B:235 , SER B:260 , LEU B:261 , GLY B:282 , ILE B:283 , GLY B:284 , PRO B:286 , LEU B:310 , THR B:343 , ASP B:346 , GLY B:480 , ASP B:481 , ASN B:487 , THR B:488 , THR B:489 , SER B:492 , HOH B:2400 , HOH B:2406 , HOH B:3213 , HOH B:3214 , HOH B:3215 , HOH B:3216 , HOH B:3217 , HOH B:3218 , HOH B:3219 , HOH B:3220
BINDING SITE FOR RESIDUE FAD B1031
14
BC5
SOFTWARE
ASN B:609 , GLU B:611 , ASN B:668 , SER B:670 , ASN B:736 , THR B:737 , FMN B:1030 , HOH B:2825 , HOH B:3212
BINDING SITE FOR RESIDUE IUR B1034
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (A:69-100,B:69-100,A:944-976,B:944-...)
2: 4FE4S_FER_1 (A:986-997,B:986-997)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
DPYD_PIG
69-100
944-976
978-1007
6
A:69-100
B:69-100
-
-
A:944-976
B:944-976
-
-
A:978-1007
B:978-1007
-
-
2
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
DPYD_PIG
986-997
2
A:986-997
B:986-997
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 20)
Info
All SCOP Domains
1a: SCOP_d1gtea1 (A:2-183)
1b: SCOP_d1gteb1 (B:2-183)
1c: SCOP_d1gtec1 (C:2-183)
1d: SCOP_d1gted1 (D:2-183)
2a: SCOP_d1gtea5 (A:845-1017)
2b: SCOP_d1gteb5 (B:845-1018)
2c: SCOP_d1gtec5 (C:845-1017)
2d: SCOP_d1gted5 (D:845-1019)
3a: SCOP_d1gtea3 (A:288-440)
3b: SCOP_d1gteb3 (B:288-440)
3c: SCOP_d1gtec3 (C:288-440)
3d: SCOP_d1gted3 (D:288-440)
4a: SCOP_d1gtea4 (A:184-287,A:441-532)
4b: SCOP_d1gteb4 (B:184-287,B:441-532)
4c: SCOP_d1gtec4 (C:184-287,C:441-532)
4d: SCOP_d1gted4 (D:184-287,D:441-532)
5a: SCOP_d1gtea2 (A:533-844)
5b: SCOP_d1gteb2 (B:533-844)
5c: SCOP_d1gtec2 (C:533-844)
5d: SCOP_d1gted2 (D:533-844)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
alpha-helical ferredoxin
(43)
Family
:
Dihydropyrimidine dehydrogenase, N-terminal domain
(5)
Protein domain
:
Dihydropyrimidine dehydrogenase, N-terminal domain
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
1a
d1gtea1
A:2-183
1b
d1gteb1
B:2-183
1c
d1gtec1
C:2-183
1d
d1gted1
D:2-183
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Dihydropyrimidine dehydrogenase, C-terminal domain
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
2a
d1gtea5
A:845-1017
2b
d1gteb5
B:845-1018
2c
d1gtec5
C:845-1017
2d
d1gted5
D:845-1019
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
C-terminal domain of adrenodoxin reductase-like
(19)
Protein domain
:
Dihydropyrimidine dehydrogenase, domain 3
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
3a
d1gtea3
A:288-440
3b
d1gteb3
B:288-440
3c
d1gtec3
C:288-440
3d
d1gted3
D:288-440
Fold
:
Nucleotide-binding domain
(33)
Superfamily
:
Nucleotide-binding domain
(33)
Family
:
N-terminal domain of adrenodoxin reductase-like
(19)
Protein domain
:
Dihydropyrimidine dehydrogenase, domain 2
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
4a
d1gtea4
A:184-287,A:441-532
4b
d1gteb4
B:184-287,B:441-532
4c
d1gtec4
C:184-287,C:441-532
4d
d1gted4
D:184-287,D:441-532
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
FMN-linked oxidoreductases
(290)
Family
:
FMN-linked oxidoreductases
(242)
Protein domain
:
Dihydropyrimidine dehydrogenase, domain 4
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
5a
d1gtea2
A:533-844
5b
d1gteb2
B:533-844
5c
d1gtec2
C:533-844
5d
d1gted2
D:533-844
[
close SCOP info
]
CATH Domains
(4, 20)
Info
all CATH domains
1a: CATH_1gteA01 (A:2-26,A:934-1017)
1b: CATH_1gteC01 (C:2-26,C:934-1017)
1c: CATH_1gteB01 (B:2-26,B:934-1018)
1d: CATH_1gteD01 (D:2-26,D:934-1019)
2a: CATH_1gteA03 (A:184-287,A:441-532)
2b: CATH_1gteB03 (B:184-287,B:441-532)
2c: CATH_1gteA04 (A:288-440)
2d: CATH_1gteB04 (B:288-440)
2e: CATH_1gteC04 (C:288-440)
2f: CATH_1gteD04 (D:288-440)
2g: CATH_1gteC03 (C:184-287,C:441-532)
2h: CATH_1gteD03 (D:184-287,D:441-532)
3a: CATH_1gteB05 (B:533-844)
3b: CATH_1gteC05 (C:533-844)
3c: CATH_1gteA05 (A:533-844)
3d: CATH_1gteD05 (D:533-844)
4a: CATH_1gteA02 (A:27-183)
4b: CATH_1gteB02 (B:27-183)
4c: CATH_1gteC02 (C:27-183)
4d: CATH_1gteD02 (D:27-183)
View:
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Classes
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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.20, no name defined]
(120)
Pig (Sus scrofa)
(3)
1a
1gteA01
A:2-26,A:934-1017
1b
1gteC01
C:2-26,C:934-1017
1c
1gteB01
B:2-26,B:934-1018
1d
1gteD01
D:2-26,D:934-1019
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Pig (Sus scrofa)
(5)
2a
1gteA03
A:184-287,A:441-532
2b
1gteB03
B:184-287,B:441-532
2c
1gteA04
A:288-440
2d
1gteB04
B:288-440
2e
1gteC04
C:288-440
2f
1gteD04
D:288-440
2g
1gteC03
C:184-287,C:441-532
2h
1gteD03
D:184-287,D:441-532
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Pig (Sus scrofa)
(3)
3a
1gteB05
B:533-844
3b
1gteC05
C:533-844
3c
1gteA05
A:533-844
3d
1gteD05
D:533-844
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Homologous Superfamily
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Pig (Sus scrofa)
(5)
4a
1gteA02
A:27-183
4b
1gteB02
B:27-183
4c
1gteC02
C:27-183
4d
1gteD02
D:27-183
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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