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1DDO
Asym. Unit
Info
Asym.Unit (467 KB)
Biol.Unit 1 (120 KB)
Biol.Unit 2 (120 KB)
Biol.Unit 3 (119 KB)
Biol.Unit 4 (119 KB)
Biol.Unit 5 (231 KB)
Biol.Unit 6 (232 KB)
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(1)
Title
:
REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP
Authors
:
F. Todone, A. Mattevi
Date
:
16 Jan 97 (Deposition) - 23 Jul 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,G (1x)
Biol. Unit 4: D,H (1x)
Biol. Unit 5: C,D,G,H (1x)
Biol. Unit 6: A,B,E,F (1x)
Keywords
:
Flavoenzyme, Fad Cofactor, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Todone, M. A. Vanoni, A. Mozzarelli, M. Bolognesi, A. Coda, B. Curti, A. Mattevi
Active Site Plasticity In D-Amino Acid Oxidase: A Crystallographic Analysis.
Biochemistry V. 36 5853 1997
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(3, 18)
Info
All Hetero Components
1a: D-TRYPTOPHAN (DTRa)
1b: D-TRYPTOPHAN (DTRb)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
2f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
2g: FLAVIN-ADENINE DINUCLEOTIDE (FADg)
2h: FLAVIN-ADENINE DINUCLEOTIDE (FADh)
3a: IMINO-TRYPTOPHAN (ITRa)
3b: IMINO-TRYPTOPHAN (ITRb)
3c: IMINO-TRYPTOPHAN (ITRc)
3d: IMINO-TRYPTOPHAN (ITRd)
3e: IMINO-TRYPTOPHAN (ITRe)
3f: IMINO-TRYPTOPHAN (ITRf)
3g: IMINO-TRYPTOPHAN (ITRg)
3h: IMINO-TRYPTOPHAN (ITRh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTR
2
Ligand/Ion
D-TRYPTOPHAN
2
FAD
8
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
ITR
8
Ligand/Ion
IMINO-TRYPTOPHAN
[
close Hetero Component info
]
Sites
(26, 26)
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: FAA (UNKNOWN)
20: FAB (UNKNOWN)
21: FAC (UNKNOWN)
22: FAD (UNKNOWN)
23: FAE (UNKNOWN)
24: FAF (UNKNOWN)
25: FAG (UNKNOWN)
26: FAH (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:7 , ALA A:8 , GLY A:9 , VAL A:10 , ILE A:11 , ALA A:36 , ASP A:37 , ARG A:38 , THR A:43 , THR A:44 , THR A:45 , VAL A:47 , ALA A:48 , ALA A:49 , GLY A:50 , LEU A:51 , ARG A:162 , LYS A:163 , VAL A:164 , CYS A:181 , THR A:182 , TRP A:185 , GLY A:281 , ARG A:283 , GLY A:312 , GLY A:313 , TYR A:314 , GLY A:315 , LEU A:316 , THR A:317 , ITR A:349 , HOH A:361 , HOH A:364
BINDING SITE FOR RESIDUE FAD A 348
02
AC2
SOFTWARE
GLN A:53 , PRO A:54 , HIS A:217 , TYR A:228 , ARG A:283 , GLY A:313 , FAD A:348
BINDING SITE FOR RESIDUE ITR A 349
03
AC3
SOFTWARE
GLY B:7 , ALA B:8 , GLY B:9 , VAL B:10 , ILE B:11 , ALA B:36 , ASP B:37 , ARG B:38 , THR B:43 , THR B:44 , THR B:45 , VAL B:47 , ALA B:48 , ALA B:49 , GLY B:50 , LEU B:51 , ARG B:162 , LYS B:163 , VAL B:164 , CYS B:181 , THR B:182 , TRP B:185 , GLY B:281 , ARG B:283 , GLY B:312 , GLY B:313 , TYR B:314 , GLY B:315 , LEU B:316 , THR B:317 , ITR B:349
BINDING SITE FOR RESIDUE FAD B 348
04
AC4
SOFTWARE
GLN B:53 , PRO B:54 , TYR B:224 , TYR B:228 , ARG B:283 , GLY B:313 , FAD B:348
BINDING SITE FOR RESIDUE ITR B 349
05
AC5
SOFTWARE
GLY C:7 , ALA C:8 , GLY C:9 , VAL C:10 , ILE C:11 , ALA C:36 , ASP C:37 , ARG C:38 , THR C:43 , THR C:44 , THR C:45 , VAL C:47 , ALA C:48 , ALA C:49 , GLY C:50 , LEU C:51 , ARG C:162 , LYS C:163 , VAL C:164 , CYS C:181 , THR C:182 , TRP C:185 , GLY C:281 , ARG C:283 , GLY C:312 , GLY C:313 , TYR C:314 , GLY C:315 , LEU C:316 , THR C:317 , ITR C:349
BINDING SITE FOR RESIDUE FAD C 348
06
AC6
SOFTWARE
GLN C:53 , PRO C:54 , HIS C:217 , TYR C:228 , ARG C:283 , GLY C:313 , FAD C:348
BINDING SITE FOR RESIDUE ITR C 349
07
AC7
SOFTWARE
GLY D:7 , ALA D:8 , GLY D:9 , VAL D:10 , ILE D:11 , ALA D:36 , ASP D:37 , ARG D:38 , THR D:43 , THR D:44 , THR D:45 , VAL D:47 , ALA D:48 , ALA D:49 , GLY D:50 , LEU D:51 , ARG D:162 , LYS D:163 , VAL D:164 , CYS D:181 , THR D:182 , TRP D:185 , GLY D:281 , ARG D:283 , GLY D:312 , GLY D:313 , TYR D:314 , GLY D:315 , LEU D:316 , THR D:317 , ITR D:349 , HOH D:352
BINDING SITE FOR RESIDUE FAD D 348
08
AC8
SOFTWARE
GLN D:53 , PRO D:54 , HIS D:217 , ILE D:223 , TYR D:224 , TYR D:228 , ARG D:283 , GLY D:313 , FAD D:348
BINDING SITE FOR RESIDUE ITR D 349
09
AC9
SOFTWARE
GLY E:7 , ALA E:8 , GLY E:9 , VAL E:10 , ILE E:11 , ALA E:36 , ASP E:37 , ARG E:38 , THR E:43 , THR E:44 , THR E:45 , VAL E:47 , ALA E:48 , ALA E:49 , GLY E:50 , LEU E:51 , ARG E:162 , LYS E:163 , VAL E:164 , CYS E:181 , THR E:182 , TRP E:185 , GLY E:281 , ARG E:283 , GLY E:312 , GLY E:313 , TYR E:314 , GLY E:315 , LEU E:316 , THR E:317 , ITR E:349
BINDING SITE FOR RESIDUE FAD E 348
10
BC1
SOFTWARE
GLN E:53 , PRO E:54 , TYR E:228 , ARG E:283 , GLY E:313 , FAD E:348
BINDING SITE FOR RESIDUE ITR E 349
11
BC2
SOFTWARE
GLY F:7 , ALA F:8 , GLY F:9 , VAL F:10 , ILE F:11 , ALA F:36 , ASP F:37 , ARG F:38 , THR F:43 , THR F:44 , THR F:45 , VAL F:47 , ALA F:48 , ALA F:49 , GLY F:50 , LEU F:51 , ARG F:162 , LYS F:163 , VAL F:164 , CYS F:181 , THR F:182 , TRP F:185 , GLY F:281 , ARG F:283 , GLY F:312 , GLY F:313 , TYR F:314 , GLY F:315 , LEU F:316 , THR F:317 , ITR F:349 , HOH F:364 , HOH F:369
BINDING SITE FOR RESIDUE FAD F 348
12
BC3
SOFTWARE
GLN F:53 , PRO F:54 , HIS F:217 , ILE F:223 , TYR F:224 , TYR F:228 , ARG F:283 , GLY F:313 , FAD F:348
BINDING SITE FOR RESIDUE ITR F 349
13
BC4
SOFTWARE
GLY G:7 , ALA G:8 , GLY G:9 , VAL G:10 , ILE G:11 , ALA G:36 , ASP G:37 , ARG G:38 , THR G:43 , THR G:44 , THR G:45 , VAL G:47 , ALA G:48 , ALA G:49 , GLY G:50 , LEU G:51 , ARG G:162 , LYS G:163 , VAL G:164 , CYS G:181 , THR G:182 , TRP G:185 , GLY G:281 , ARG G:283 , GLY G:312 , GLY G:313 , TYR G:314 , GLY G:315 , LEU G:316 , THR G:317 , ITR G:349
BINDING SITE FOR RESIDUE FAD G 348
14
BC5
SOFTWARE
GLN G:53 , PRO G:54 , TYR G:224 , TYR G:228 , ARG G:283 , GLY G:313 , FAD G:348
BINDING SITE FOR RESIDUE ITR G 349
15
BC6
SOFTWARE
GLY H:7 , ALA H:8 , GLY H:9 , VAL H:10 , ILE H:11 , ALA H:36 , ASP H:37 , ARG H:38 , THR H:43 , THR H:44 , THR H:45 , VAL H:47 , ALA H:48 , ALA H:49 , GLY H:50 , LEU H:51 , ARG H:162 , LYS H:163 , VAL H:164 , CYS H:181 , THR H:182 , TRP H:185 , GLY H:281 , ARG H:283 , GLY H:312 , GLY H:313 , TYR H:314 , GLY H:315 , LEU H:316 , THR H:317 , ITR H:349
BINDING SITE FOR RESIDUE FAD H 348
16
BC7
SOFTWARE
GLN H:53 , PRO H:54 , TYR H:228 , ARG H:283 , GLY H:313 , FAD H:348
BINDING SITE FOR RESIDUE ITR H 349
17
BC8
SOFTWARE
GLU A:169 , ARG E:2 , ASP E:31 , LYS E:33 , GLY E:173
BINDING SITE FOR RESIDUE DTR E 350
18
BC9
SOFTWARE
GLU B:169 , ARG F:2 , ASP F:31 , LYS F:33 , GLY F:173 , GLY F:174
BINDING SITE FOR RESIDUE DTR F 350
19
FAA
UNKNOWN
FAD A:348
COFACTOR.
20
FAB
UNKNOWN
FAD B:348
COFACTOR.
21
FAC
UNKNOWN
FAD C:348
COFACTOR.
22
FAD
UNKNOWN
FAD D:348
COFACTOR.
23
FAE
UNKNOWN
FAD E:348
COFACTOR.
24
FAF
UNKNOWN
FAD F:348
COFACTOR.
25
FAG
UNKNOWN
FAD G:348
COFACTOR.
26
FAH
UNKNOWN
FAD H:348
COFACTOR.
[
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
(1, 8)
Info
All PROSITE Patterns/Profiles
1: DAO (A:305-323,B:305-323,C:305-323,D:30...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DAO
PS00677
D-amino acid oxidases signature.
OXDA_PIG
305-323
8
A:305-323
B:305-323
C:305-323
D:305-323
E:305-323
F:305-323
G:305-323
H:305-323
[
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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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1ddoa2 (A:195-287)
1b: SCOP_d1ddob2 (B:195-287)
1c: SCOP_d1ddoc2 (C:195-287)
1d: SCOP_d1ddod2 (D:195-287)
1e: SCOP_d1ddoe2 (E:195-287)
1f: SCOP_d1ddof2 (F:195-287)
1g: SCOP_d1ddog2 (G:195-287)
1h: SCOP_d1ddoh2 (H:195-287)
2a: SCOP_d1ddoa1 (A:1-194,A:288-339)
2b: SCOP_d1ddob1 (B:1-194,B:288-339)
2c: SCOP_d1ddoc1 (C:1-194,C:288-339)
2d: SCOP_d1ddod1 (D:1-194,D:288-339)
2e: SCOP_d1ddoe1 (E:1-194,E:288-339)
2f: SCOP_d1ddof1 (F:1-194,F:288-339)
2g: SCOP_d1ddog1 (G:1-194,G:288-339)
2h: SCOP_d1ddoh1 (H:1-194,H:288-339)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FAD-linked reductases, C-terminal domain
(181)
Superfamily
:
FAD-linked reductases, C-terminal domain
(181)
Family
:
D-aminoacid oxidase-like
(29)
Protein domain
:
D-aminoacid oxidase
(10)
Pig (Sus scrofa) [TaxId: 9823]
(6)
1a
d1ddoa2
A:195-287
1b
d1ddob2
B:195-287
1c
d1ddoc2
C:195-287
1d
d1ddod2
D:195-287
1e
d1ddoe2
E:195-287
1f
d1ddof2
F:195-287
1g
d1ddog2
G:195-287
1h
d1ddoh2
H:195-287
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-binding domain
(33)
Superfamily
:
Nucleotide-binding domain
(33)
Family
:
D-aminoacid oxidase, N-terminal domain
(10)
Protein domain
:
D-aminoacid oxidase, N-terminal domain
(10)
Pig (Sus scrofa) [TaxId: 9823]
(6)
2a
d1ddoa1
A:1-194,A:288-339
2b
d1ddob1
B:1-194,B:288-339
2c
d1ddoc1
C:1-194,C:288-339
2d
d1ddod1
D:1-194,D:288-339
2e
d1ddoe1
E:1-194,E:288-339
2f
d1ddof1
F:1-194,F:288-339
2g
d1ddog1
G:1-194,G:288-339
2h
d1ddoh1
H:1-194,H:288-339
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1ddoA02 (A:89-139,A:196-285)
1b: CATH_1ddoB02 (B:89-139,B:196-285)
1c: CATH_1ddoC02 (C:89-139,C:196-285)
1d: CATH_1ddoD02 (D:89-139,D:196-285)
1e: CATH_1ddoE02 (E:89-139,E:196-285)
1f: CATH_1ddoF02 (F:89-139,F:196-285)
1g: CATH_1ddoG02 (G:89-139,G:196-285)
1h: CATH_1ddoH02 (H:89-139,H:196-285)
2a: CATH_1ddoA01 (A:1-88,A:140-195,A:286-339)
2b: CATH_1ddoB01 (B:1-88,B:140-195,B:286-339)
2c: CATH_1ddoC01 (C:1-88,C:140-195,C:286-339)
2d: CATH_1ddoD01 (D:1-88,D:140-195,D:286-339)
2e: CATH_1ddoE01 (E:1-88,E:140-195,E:286-339)
2f: CATH_1ddoF01 (F:1-88,F:140-195,F:286-339)
2g: CATH_1ddoG01 (G:1-88,G:140-195,G:286-339)
2h: CATH_1ddoH01 (H:1-88,H:140-195,H:286-339)
View:
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Topologies
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(
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-Amino Acid Oxidase; Chain A, domain 2
(80)
Homologous Superfamily
:
D-Amino Acid Oxidase, subunit A, domain 2
(80)
Pig (Sus scrofa)
(6)
1a
1ddoA02
A:89-139,A:196-285
1b
1ddoB02
B:89-139,B:196-285
1c
1ddoC02
C:89-139,C:196-285
1d
1ddoD02
D:89-139,D:196-285
1e
1ddoE02
E:89-139,E:196-285
1f
1ddoF02
F:89-139,F:196-285
1g
1ddoG02
G:89-139,G:196-285
1h
1ddoH02
H:89-139,H:196-285
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Pig (Sus scrofa)
(21)
2a
1ddoA01
A:1-88,A:140-195,A:286-339
2b
1ddoB01
B:1-88,B:140-195,B:286-339
2c
1ddoC01
C:1-88,C:140-195,C:286-339
2d
1ddoD01
D:1-88,D:140-195,D:286-339
2e
1ddoE01
E:1-88,E:140-195,E:286-339
2f
1ddoF01
F:1-88,F:140-195,F:286-339
2g
1ddoG01
G:1-88,G:140-195,G:286-339
2h
1ddoH01
H:1-88,H:140-195,H:286-339
[
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Pfam Domains
(0, 0)
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