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2E4A
Asym. Unit
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
[
close Hetero Component info
]
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:
Select:
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 not available)
All SNPs/Variants
View:
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Label:
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
[
close PROSITE info
]
Exons
(10, 40)
Info
All Exons
Exon 1.2 (A:1-65 | B:1001-1065 | C:2001-2065...)
Exon 1.3 (A:65-103 | B:1065-1103 | C:2065-21...)
Exon 1.4 (A:104-129 | B:1104-1129 | C:2104-2...)
Exon 1.5 (A:129-151 | B:1129-1151 | C:2129-2...)
Exon 1.6 (A:151-169 | B:1151-1169 | C:2151-2...)
Exon 1.7 (A:170-204 | B:1170-1204 | C:2170-2...)
Exon 1.8 (A:205-232 | B:1205-1232 | C:2205-2...)
Exon 1.9 (A:232-271 | B:1232-1271 | C:2232-2...)
Exon 1.10 (A:272-304 | B:1272-1304 | C:2272-2...)
Exon 1.11 (A:305-340 | B:1305-1340 | C:2305-2...)
View:
Select:
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All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000228476
1
ENSE00001232085
chr12:
109273857-109274000
144
OXDA_HUMAN
-
0
0
-
-
1.2
ENST00000228476
2
ENSE00001232101
chr12:
109278774-109278976
203
OXDA_HUMAN
1-65
65
4
A:1-65
B:1001-1065
C:2001-2065
D:3001-3065
65
65
65
65
1.3
ENST00000228476
3
ENSE00001232078
chr12:
109281226-109281340
115
OXDA_HUMAN
65-103
39
4
A:65-103
B:1065-1103
C:2065-2103
D:3065-3103
39
39
39
39
1.4
ENST00000228476
4
ENSE00001232074
chr12:
109283245-109283321
77
OXDA_HUMAN
104-129
26
4
A:104-129
B:1104-1129
C:2104-2129
D:3104-3129
26
26
26
26
1.5
ENST00000228476
5
ENSE00001232068
chr12:
109283984-109284049
66
OXDA_HUMAN
129-151
23
4
A:129-151
B:1129-1151
C:2129-2151
D:3129-3151
23
23
23
23
1.6
ENST00000228476
6
ENSE00001232066
chr12:
109286758-109286812
55
OXDA_HUMAN
151-169
19
4
A:151-169
B:1151-1169
C:2151-2169
D:3151-3169
19
19
19
19
1.7
ENST00000228476
7
ENSE00001232061
chr12:
109288039-109288143
105
OXDA_HUMAN
170-204
35
4
A:170-204
B:1170-1204
C:2170-2204
D:3170-3204
35
35
35
35
1.8
ENST00000228476
8
ENSE00000754687
chr12:
109290782-109290864
83
OXDA_HUMAN
205-232
28
4
A:205-232
B:1205-1232
C:2205-2232
D:3205-3232
28
28
28
28
1.9
ENST00000228476
9
ENSE00001232053
chr12:
109292455-109292572
118
OXDA_HUMAN
232-271
40
4
A:232-271
B:1232-1271
C:2232-2271
D:3232-3271
40
40
40
40
1.10
ENST00000228476
10
ENSE00001232046
chr12:
109293153-109293251
99
OXDA_HUMAN
272-304
33
4
A:272-304
B:1272-1304
C:2272-2304
D:3272-3304
33
33
33
33
1.11
ENST00000228476
11
ENSE00001232095
chr12:
109294180-109294709
530
OXDA_HUMAN
305-347
43
4
A:305-340
B:1305-1340
C:2305-2340
D:3305-3340
36
36
36
36
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
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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Classes
(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
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
all PFAM domains
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