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2E4A
Biol. Unit 3
Info
Asym.Unit (234 KB)
Biol.Unit 1 (116 KB)
Biol.Unit 2 (116 KB)
Biol.Unit 3 (227 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN D-AMINO ACID OXIDASE IN COMPLEX WITH O-AMINOBENZOATE
Authors
:
T. Kawazoe, H. Tsuge, T. Imagawa, K. Fukui
Date
:
05 Dec 06 (Deposition) - 06 Mar 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Structurally Ambivalent Peptide, O-Aminobenzoate Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Kawazoe, H. Tsuge, T. Imagawa, K. Aki, S. Kuramitsu, K. Fukui
Structural Basis Of D-Dopa Oxidation By D-Amino Acid Oxidase: Alternative Pathway For Dopamine Biosynthesis.
Biochem. Biophys. Res. Commun. V. 355 385 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: 2-AMINOBENZOIC ACID (BE2a)
1b: 2-AMINOBENZOIC ACID (BE2b)
1c: 2-AMINOBENZOIC ACID (BE2c)
1d: 2-AMINOBENZOIC ACID (BE2d)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BE2
4
Ligand/Ion
2-AMINOBENZOIC ACID
2
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:7 , GLY A:9 , VAL A:10 , ILE A:11 , ASP A:37 , ARG A:38 , THR A:43 , THR A:44 , THR A:45 , ALA A:48 , GLY A:50 , LEU A:51 , ARG A:162 , LYS A:163 , VAL A:164 , THR A:182 , GLY A:183 , TRP A:185 , ARG A:283 , GLY A:312 , GLY A:313 , TYR A:314 , GLY A:315 , LEU A:316 , THR A:317 , BE2 A:352 , HOH A:380
BINDING SITE FOR RESIDUE FAD A 351
2
AC2
SOFTWARE
TYR A:224 , TYR A:228 , ILE A:230 , ARG A:283 , GLY A:313 , FAD A:351
BINDING SITE FOR RESIDUE BE2 A 352
3
AC3
SOFTWARE
HOH B:47 , HOH B:83 , HOH B:89 , GLY B:1007 , ALA B:1008 , GLY B:1009 , VAL B:1010 , ILE B:1011 , ASP B:1037 , ARG B:1038 , THR B:1044 , THR B:1045 , ALA B:1048 , GLY B:1050 , LEU B:1051 , ARG B:1162 , VAL B:1164 , THR B:1182 , GLY B:1183 , TRP B:1185 , ARG B:1283 , GLY B:1312 , GLY B:1313 , TYR B:1314 , GLY B:1315 , LEU B:1316 , THR B:1317 , BE2 B:1352
BINDING SITE FOR RESIDUE FAD B 1351
4
AC4
SOFTWARE
TYR B:1224 , TYR B:1228 , ILE B:1230 , ARG B:1283 , GLY B:1313 , FAD B:1351
BINDING SITE FOR RESIDUE BE2 B 1352
5
AC5
SOFTWARE
HOH C:54 , GLY C:2007 , GLY C:2009 , VAL C:2010 , ILE C:2011 , ASP C:2037 , ARG C:2038 , THR C:2043 , THR C:2044 , THR C:2045 , ALA C:2048 , GLY C:2050 , LEU C:2051 , ARG C:2162 , LYS C:2163 , VAL C:2164 , THR C:2182 , GLY C:2183 , TRP C:2185 , LEU C:2189 , ARG C:2283 , PRO C:2284 , GLY C:2312 , GLY C:2313 , TYR C:2314 , GLY C:2315 , LEU C:2316 , THR C:2317 , BE2 C:2352
BINDING SITE FOR RESIDUE FAD C 2351
6
AC6
SOFTWARE
LEU C:2215 , TYR C:2224 , TYR C:2228 , ILE C:2230 , ARG C:2283 , GLY C:2313 , FAD C:2351
BINDING SITE FOR RESIDUE BE2 C 2352
7
AC7
SOFTWARE
HOH D:49 , HOH D:92 , GLY D:3007 , ALA D:3008 , GLY D:3009 , VAL D:3010 , ILE D:3011 , ALA D:3036 , ASP D:3037 , ARG D:3038 , THR D:3043 , THR D:3044 , THR D:3045 , ALA D:3048 , GLY D:3050 , LEU D:3051 , ARG D:3162 , VAL D:3164 , THR D:3182 , GLY D:3183 , LEU D:3189 , ARG D:3283 , PRO D:3284 , GLY D:3312 , GLY D:3313 , TYR D:3314 , GLY D:3315 , LEU D:3316 , THR D:3317 , BE2 D:3352
BINDING SITE FOR RESIDUE FAD D 3351
8
AC8
SOFTWARE
TYR D:3224 , TYR D:3228 , ILE D:3230 , ARG D:3283 , GLY D:3313 , FAD D:3351
BINDING SITE FOR RESIDUE BE2 D 3352
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: DAO (A:305-323,B:1305-1323,C:2305-2323,...)
;
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_HUMAN
305-323
4
A:305-323
B:1305-1323
C:2305-2323
D:3305-3323
[
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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
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2e4aA02 (A:89-139,A:196-285)
1b: CATH_2e4aC02 (C:2089-2139,C:2196-2285)
1c: CATH_2e4aD02 (D:3089-3139,D:3196-3285)
1d: CATH_2e4aB02 (B:1089-1139,B:1196-1285)
2a: CATH_2e4aA01 (A:1-88,A:140-195,A:286-340)
2b: CATH_2e4aB01 (B:1001-1088,B:1140-1195,B:1286-1340)
2c: CATH_2e4aC01 (C:2001-2088,C:2140-2195,C:2286-2340)
2d: CATH_2e4aD01 (D:3001-3088,D:3140-3195,D:3286-3340)
View:
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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)
Human (Homo sapiens)
(6)
1a
2e4aA02
A:89-139,A:196-285
1b
2e4aC02
C:2089-2139,C:2196-2285
1c
2e4aD02
D:3089-3139,D:3196-3285
1d
2e4aB02
B:1089-1139,B:1196-1285
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
2e4aA01
A:1-88,A:140-195,A:286-340
2b
2e4aB01
B:1001-1088,B:1140-1195,B:1286-1340
2c
2e4aC01
C:2001-2088,C:2140-2195,C:2286-2340
2d
2e4aD01
D:3001-3088,D:3140-3195,D:3286-3340
[
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Pfam Domains
(0, 0)
Info
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Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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Show PDB file:
Asym.Unit (234 KB)
Header - Asym.Unit
Biol.Unit 1 (116 KB)
Header - Biol.Unit 1
Biol.Unit 2 (116 KB)
Header - Biol.Unit 2
Biol.Unit 3 (227 KB)
Header - Biol.Unit 3
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