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1TB3
Asym. Unit
Info
Asym.Unit (446 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (223 KB)
Biol.Unit 3 (438 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF RECOMBINANT RAT KIDNEY LONG-CHAIN HYDROXY ACID OXIDASE
Authors
:
L. M. Cunane, J. D. Barton, Z. W. Chen, K. H. D. Le, D. Amar, F. Lederer, F. S. Mathews
Date
:
19 May 04 (Deposition) - 01 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: A,B,C,D,E,F,G,H (1x)
Keywords
:
Long Chain Alpha-Hydroxy Acid Oxidase, Flavoprotein, Oxidase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. M. Cunane, J. D. Barton, Z. W. Chen, K. H. D. Le, D. Amar, F. Lederer, F. S. Mathews
Crystal Structure Analysis Of Recombinant Rat Kidney Long Chain Hydroxy Acid Oxidase.
Biochemistry V. 44 1521 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
1d: ACETIC ACID (ACYd)
1e: ACETIC ACID (ACYe)
1f: ACETIC ACID (ACYf)
1g: ACETIC ACID (ACYg)
1h: ACETIC ACID (ACYh)
2a: FLAVIN MONONUCLEOTIDE (FMNa)
2b: FLAVIN MONONUCLEOTIDE (FMNb)
2c: FLAVIN MONONUCLEOTIDE (FMNc)
2d: FLAVIN MONONUCLEOTIDE (FMNd)
2e: FLAVIN MONONUCLEOTIDE (FMNe)
2f: FLAVIN MONONUCLEOTIDE (FMNf)
2g: FLAVIN MONONUCLEOTIDE (FMNg)
2h: FLAVIN MONONUCLEOTIDE (FMNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
8
Ligand/Ion
ACETIC ACID
2
FMN
8
Ligand/Ion
FLAVIN MONONUCLEOTIDE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:23 , ILE A:24 , PRO A:76 , THR A:77 , ALA A:78 , SER A:105 , GLN A:127 , TYR A:129 , THR A:155 , LYS A:223 , SER A:245 , HIS A:247 , ARG A:250 , ASP A:278 , GLY A:279 , GLY A:280 , ARG A:282 , GLY A:301 , ARG A:302 , LEU A:305 , ACY A:1402 , HOH A:1410 , HOH A:1415
BINDING SITE FOR RESIDUE FMN A 1401
02
AC2
SOFTWARE
PHE B:23 , ILE B:24 , PRO B:76 , THR B:77 , ALA B:78 , SER B:105 , GLN B:127 , TYR B:129 , THR B:155 , LYS B:223 , SER B:245 , HIS B:247 , ARG B:250 , ASP B:278 , GLY B:279 , GLY B:280 , ARG B:282 , GLY B:301 , ARG B:302 , LEU B:305 , ACY B:2402 , HOH B:2411 , HOH B:2423
BINDING SITE FOR RESIDUE FMN B 2401
03
AC3
SOFTWARE
PHE C:23 , ILE C:24 , PRO C:76 , THR C:77 , ALA C:78 , SER C:105 , GLN C:127 , TYR C:129 , THR C:155 , LYS C:223 , SER C:245 , HIS C:247 , ARG C:250 , ASP C:278 , GLY C:279 , GLY C:280 , ARG C:282 , GLY C:301 , ARG C:302 , LEU C:305 , ACY C:3402 , HOH C:3405 , HOH C:3445
BINDING SITE FOR RESIDUE FMN C 3401
04
AC4
SOFTWARE
PHE D:23 , ILE D:24 , PRO D:76 , THR D:77 , ALA D:78 , SER D:105 , GLN D:127 , TYR D:129 , THR D:155 , LYS D:223 , SER D:245 , HIS D:247 , ARG D:250 , ASP D:278 , GLY D:279 , GLY D:280 , ARG D:282 , GLY D:301 , ARG D:302 , LEU D:305 , ACY D:4402 , HOH D:4421 , HOH D:4422
BINDING SITE FOR RESIDUE FMN D 4401
05
AC5
SOFTWARE
PHE E:23 , ILE E:24 , SER E:75 , PRO E:76 , THR E:77 , ALA E:78 , SER E:105 , GLN E:127 , TYR E:129 , THR E:155 , LYS E:223 , SER E:245 , HIS E:247 , GLY E:248 , ARG E:250 , ASP E:278 , GLY E:279 , GLY E:280 , ARG E:282 , GLY E:301 , ARG E:302 , LEU E:305 , ACY E:5402 , HOH E:5425 , HOH E:5426
BINDING SITE FOR RESIDUE FMN E 5401
06
AC6
SOFTWARE
PHE F:23 , ILE F:24 , PRO F:76 , THR F:77 , ALA F:78 , SER F:105 , GLN F:127 , TYR F:129 , THR F:155 , LYS F:223 , SER F:245 , HIS F:247 , ARG F:250 , ASP F:278 , GLY F:279 , GLY F:280 , ARG F:282 , GLY F:301 , ARG F:302 , LEU F:305 , ACY F:6402 , HOH F:6408 , HOH F:6421
BINDING SITE FOR RESIDUE FMN F 6401
07
AC7
SOFTWARE
PHE G:23 , ILE G:24 , PRO G:76 , THR G:77 , ALA G:78 , SER G:105 , GLN G:127 , TYR G:129 , THR G:155 , LYS G:223 , SER G:245 , HIS G:247 , ARG G:250 , ASP G:278 , GLY G:279 , GLY G:280 , ARG G:282 , GLY G:301 , ARG G:302 , LEU G:305 , ACY G:7402 , HOH G:7409 , HOH G:7427
BINDING SITE FOR RESIDUE FMN G 7401
08
AC8
SOFTWARE
PHE H:23 , ILE H:24 , PRO H:76 , THR H:77 , ALA H:78 , SER H:105 , GLN H:127 , TYR H:129 , THR H:155 , LYS H:223 , SER H:245 , HIS H:247 , ARG H:250 , ASP H:278 , GLY H:279 , GLY H:280 , ARG H:282 , GLY H:301 , ARG H:302 , LEU H:305 , ACY H:8402 , HOH H:8403 , HOH H:8441
BINDING SITE FOR RESIDUE FMN H 8401
09
AC9
SOFTWARE
TYR A:129 , ARG A:164 , HIS A:247 , ARG A:250 , FMN A:1401
BINDING SITE FOR RESIDUE ACY A 1402
10
BC1
SOFTWARE
TYR B:129 , ARG B:164 , HIS B:247 , ARG B:250 , FMN B:2401
BINDING SITE FOR RESIDUE ACY B 2402
11
BC2
SOFTWARE
TYR C:129 , ARG C:164 , HIS C:247 , FMN C:3401
BINDING SITE FOR RESIDUE ACY C 3402
12
BC3
SOFTWARE
TYR D:129 , ARG D:164 , HIS D:247 , FMN D:4401
BINDING SITE FOR RESIDUE ACY D 4402
13
BC4
SOFTWARE
TYR E:129 , ARG E:164 , HIS E:247 , ARG E:250 , FMN E:5401
BINDING SITE FOR RESIDUE ACY E 5402
14
BC5
SOFTWARE
TYR F:129 , ARG F:164 , HIS F:247 , ARG F:250 , FMN F:6401
BINDING SITE FOR RESIDUE ACY F 6402
15
BC6
SOFTWARE
TYR G:129 , ARG G:164 , HIS G:247 , FMN G:7401
BINDING SITE FOR RESIDUE ACY G 7402
16
BC7
SOFTWARE
TYR H:129 , ARG H:164 , HIS H:247 , FMN H:8401
BINDING SITE FOR RESIDUE ACY H 8402
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: FMN_HYDROXY_ACID_DH_1 (A:245-251,B:245-251,C:245-251,D:24...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FMN_HYDROXY_ACID_DH_1
PS00557
FMN-dependent alpha-hydroxy acid dehydrogenases active site.
HAOX2_RAT
246-252
8
A:245-251
B:245-251
C:245-251
D:245-251
E:245-251
F:245-251
G:245-251
H:245-251
[
close PROSITE info
]
Exons
(7, 56)
Info
All Exons
Exon 1.3 (A:1-43 | B:1-43 | C:1-43 | D:1-43 ...)
Exon 1.4 (A:43-94 | B:43-94 | C:43-94 | D:43...)
Exon 1.5 (A:94-188 (gaps) | B:94-187 (gaps) ...)
Exon 1.6 (A:202-258 | B:202-258 | C:202-258 ...)
Exon 1.7 (A:259-311 | B:259-311 | C:259-311 ...)
Exon 1.8 (A:312-335 | B:312-335 | C:312-335 ...)
Exon 1.9 (A:335-349 | B:335-349 | C:335-349 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3
2: Boundary 1.3/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6
5: Boundary 1.6/1.7
6: Boundary 1.7/1.8
7: Boundary 1.8/1.9
8: Boundary 1.9/-
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
ENSRNOT00000046942
1
ENSRNOE00000330508
chr2:
193557229-193557142
88
HAOX2_RAT
-
0
0
-
-
1.2
ENSRNOT00000046942
2
ENSRNOE00000336299
chr2:
193549512-193549408
105
HAOX2_RAT
-
0
0
-
-
1.3
ENSRNOT00000046942
3
ENSRNOE00000188996
chr2:
193548657-193548519
139
HAOX2_RAT
1-44
44
8
A:1-43
B:1-43
C:1-43
D:1-43
E:1-43
F:1-43
G:1-43
H:1-43
43
43
43
43
43
43
43
43
1.4
ENSRNOT00000046942
4
ENSRNOE00000189030
chr2:
193547532-193547381
152
HAOX2_RAT
44-95
52
8
A:43-94
B:43-94
C:43-94
D:43-94
E:43-94
F:43-94
G:43-94
H:43-94
52
52
52
52
52
52
52
52
1.5
ENSRNOT00000046942
5
ENSRNOE00000189057
chr2:
193546078-193545795
284
HAOX2_RAT
95-189
95
8
A:94-188 (gaps)
B:94-187 (gaps)
C:94-188 (gaps)
D:94-187 (gaps)
E:94-176
F:94-188 (gaps)
G:94-188 (gaps)
H:94-188 (gaps)
95
94
95
94
83
95
95
95
1.6
ENSRNOT00000046942
6
ENSRNOE00000189087
chr2:
193544624-193544415
210
HAOX2_RAT
190-259
70
8
A:202-258
B:202-258
C:202-258
D:202-258
E:202-258
F:202-258
G:202-258
H:202-258
57
57
57
57
57
57
57
57
1.7
ENSRNOT00000046942
7
ENSRNOE00000189115
chr2:
193534744-193534586
159
HAOX2_RAT
260-312
53
8
A:259-311
B:259-311
C:259-311
D:259-311
E:259-311
F:259-311
G:259-311
H:259-311
53
53
53
53
53
53
53
53
1.8
ENSRNOT00000046942
8
ENSRNOE00000189146
chr2:
193534270-193534201
70
HAOX2_RAT
313-336
24
8
A:312-335
B:312-335
C:312-335
D:312-335
E:312-335
F:312-335
G:312-335
H:312-335
24
24
24
24
24
24
24
24
1.9
ENSRNOT00000046942
9
ENSRNOE00000340820
chr2:
193533272-193532833
440
HAOX2_RAT
336-353
18
8
A:335-349
B:335-349
C:335-349
D:335-349
E:335-349
F:335-349
G:335-349
H:335-349
15
15
15
15
15
15
15
15
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1tb3b_ (B:)
1b: SCOP_d1tb3c_ (C:)
1c: SCOP_d1tb3d_ (D:)
1d: SCOP_d1tb3e_ (E:)
1e: SCOP_d1tb3f_ (F:)
1f: SCOP_d1tb3g_ (G:)
1g: SCOP_d1tb3h_ (H:)
2a: SCOP_d1tb3a1 (A:1-349)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
FMN-linked oxidoreductases
(290)
Family
:
automated matches
(48)
Protein domain
:
automated matches
(48)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
1a
d1tb3b_
B:
1b
d1tb3c_
C:
1c
d1tb3d_
D:
1d
d1tb3e_
E:
1e
d1tb3f_
F:
1f
d1tb3g_
G:
1g
d1tb3h_
H:
Family
:
FMN-linked oxidoreductases
(242)
Protein domain
:
Hydroxyacid oxidase
(1)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
2a
d1tb3a1
A:1-349
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1tb3E00 (E:1-349)
1b: CATH_1tb3B00 (B:1-349)
1c: CATH_1tb3D00 (D:1-349)
1d: CATH_1tb3G00 (G:1-349)
1e: CATH_1tb3A00 (A:1-349)
1f: CATH_1tb3C00 (C:1-349)
1g: CATH_1tb3F00 (F:1-349)
1h: CATH_1tb3H00 (H:1-349)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Norway rat (Rattus norvegicus)
(1)
1a
1tb3E00
E:1-349
1b
1tb3B00
B:1-349
1c
1tb3D00
D:1-349
1d
1tb3G00
G:1-349
1e
1tb3A00
A:1-349
1f
1tb3C00
C:1-349
1g
1tb3F00
F:1-349
1h
1tb3H00
H:1-349
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_FMN_dh_1tb3H01 (H:12-349)
1b: PFAM_FMN_dh_1tb3H02 (H:12-349)
1c: PFAM_FMN_dh_1tb3H03 (H:12-349)
1d: PFAM_FMN_dh_1tb3H04 (H:12-349)
1e: PFAM_FMN_dh_1tb3H05 (H:12-349)
1f: PFAM_FMN_dh_1tb3H06 (H:12-349)
1g: PFAM_FMN_dh_1tb3H07 (H:12-349)
1h: PFAM_FMN_dh_1tb3H08 (H:12-349)
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Clan
:
TIM_barrel
(694)
Family
:
FMN_dh
(23)
Rattus norvegicus (Rat)
(1)
1a
FMN_dh-1tb3H01
H:12-349
1b
FMN_dh-1tb3H02
H:12-349
1c
FMN_dh-1tb3H03
H:12-349
1d
FMN_dh-1tb3H04
H:12-349
1e
FMN_dh-1tb3H05
H:12-349
1f
FMN_dh-1tb3H06
H:12-349
1g
FMN_dh-1tb3H07
H:12-349
1h
FMN_dh-1tb3H08
H:12-349
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