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1JNQ
Biol. Unit 1
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Asym.Unit (155 KB)
Biol.Unit 1 (149 KB)
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(1)
Title
:
LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH EPIGALLOCATHECHIN (EGC)
Authors
:
K. Zhou, E. Skrzypczak-Jankun, J. Jankun
Date
:
24 Jul 01 (Deposition) - 03 Jun 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Metalloprotein, Fe(Ii) Complex, Purple Lipoxygenase, Catechin Inhibitor, Green Tea, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Skrzypczak-Jankun, K. Zhou, J. Jankun
Inhibition Of Lipoxygenase By (-)-Epigallocatechin Gallate: X-Ray Analysis At 2. 1 A Reveals Degradation Of Egcg And Shows Soybean Lox-3 Complex With Egc Instead.
Int. J. Mol. Med. V. 12 415 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMA... (EGTa)
2a: FE (II) ION (FE2a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EGT
1
Ligand/Ion
2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMAN-3,5,7-TRIOL
2
FE2
1
Ligand/Ion
FE (II) ION
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:518 , HIS A:523 , HIS A:709 , ILE A:857 , EGT A:871
BINDING SITE FOR RESIDUE FE2 A 858
2
AC2
SOFTWARE
GLN A:514 , HIS A:518 , TRP A:519 , HIS A:523 , ILE A:557 , LEU A:565 , ILE A:572 , PHE A:576 , GLN A:716 , VAL A:769 , LEU A:773 , ILE A:857 , FE2 A:858 , HOH A:1295 , HOH A:1341
BINDING SITE FOR RESIDUE EGT A 871
[
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SAPs(SNPs)/Variants
(7, 7)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_LOX3_SOYBN_001 (D25D, chain A, )
2: VAR_LOX3_SOYBN_002 (S57S, chain A, )
3: VAR_LOX3_SOYBN_003 (P112P, chain A, )
4: VAR_LOX3_SOYBN_004 (I201I, chain A, )
5: VAR_LOX3_SOYBN_005 (D382D, chain A, )
6: VAR_LOX3_SOYBN_006 (D428D, chain A, )
7: VAR_LOX3_SOYBN_007 (T630T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_LOX3_SOYBN_001
*
H
25
D
LOX3_SOYBN
---
---
A
D
25
D
2
UniProt
VAR_LOX3_SOYBN_002
*
P
57
S
LOX3_SOYBN
---
---
A
S
57
S
3
UniProt
VAR_LOX3_SOYBN_003
*
L
112
P
LOX3_SOYBN
---
---
A
P
112
P
4
UniProt
VAR_LOX3_SOYBN_004
*
V
201
I
LOX3_SOYBN
---
---
A
I
201
I
5
UniProt
VAR_LOX3_SOYBN_005
*
E
382
D
LOX3_SOYBN
---
---
A
D
382
D
6
UniProt
VAR_LOX3_SOYBN_006
*
G
428
D
LOX3_SOYBN
---
---
A
D
428
D
7
UniProt
VAR_LOX3_SOYBN_007
*
A
630
T
LOX3_SOYBN
---
---
A
T
630
T
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: PLAT (A:38-163)
2: LIPOXYGENASE_3 (A:166-857)
3: LIPOXYGENASE_1 (A:513-527)
4: LIPOXYGENASE_2 (A:540-550)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PLAT
PS50095
PLAT domain profile.
LOX3_SOYBN
38-163
1
A:38-163
2
LIPOXYGENASE_3
PS51393
Lipoxygenase iron-binding catalytic domain profile.
LOX3_SOYBN
166-857
1
A:166-857
3
LIPOXYGENASE_1
PS00711
Lipoxygenases iron-binding region signature 1.
LOX3_SOYBN
513-527
1
A:513-527
4
LIPOXYGENASE_2
PS00081
Lipoxygenases iron-binding region signature 2.
LOX3_SOYBN
540-550
1
A:540-550
[
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Exons
(0, 0)
Info
All Exons
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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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1jnqa1 (A:168-857)
2a: SCOP_d1jnqa2 (A:9-167)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Lipoxigenase
(27)
Superfamily
:
Lipoxigenase
(27)
Family
:
Plant lipoxigenases
(25)
Protein domain
:
Lipoxigenase, C-terminal domain
(23)
Soybean (Glycine max), isozyme L3 [TaxId: 3847]
(9)
1a
d1jnqa1
A:168-857
Class
:
All beta proteins
(24004)
Fold
:
Lipase/lipooxygenase domain (PLAT/LH2 domain)
(47)
Superfamily
:
Lipase/lipooxygenase domain (PLAT/LH2 domain)
(47)
Family
:
Lipoxigenase N-terminal domain
(24)
Protein domain
:
Plant lipoxigenase
(23)
Soybean (Glycine max), isozyme L3 [TaxId: 3847]
(9)
2a
d1jnqa2
A:9-167
[
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CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1jnqA04 (A:357-490)
2a: CATH_1jnqA02 (A:168-267)
3a: CATH_1jnqA03 (A:268-356)
4a: CATH_1jnqA05 (A:491-856)
5a: CATH_1jnqA01 (A:9-167)
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(
)
(
)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.60, no name defined]
(26)
Soybean (Glycine max)
(24)
1a
1jnqA04
A:357-490
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Lipoxygenase-1; domain 2
(24)
Homologous Superfamily
:
Lipoxygenase-1; Domain 2
(24)
Soybean (Glycine max)
(24)
2a
1jnqA02
A:168-267
Topology
:
Lipoxygenase-1; domain 3
(24)
Homologous Superfamily
:
Lipoxygenase-1; Domain 3
(24)
Soybean (Glycine max)
(24)
3a
1jnqA03
A:268-356
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Lipoxygenase-1; domain 5
(26)
Homologous Superfamily
:
Lipoxygenase-1; Domain 5
(26)
Soybean (Glycine max)
(24)
4a
1jnqA05
A:491-856
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Lipoxygenase-1
(46)
Homologous Superfamily
:
Lipoxygenase-1
(44)
Soybean (Glycine max)
(24)
5a
1jnqA01
A:9-167
[
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]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_PLAT_1jnqA01 (A:58-162)
2a: PFAM_Lipoxygenase_1jnqA02 (A:173-841)
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Clans
(
)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
PLAT
(25)
Family
:
PLAT
(25)
Glycine max (Soybean) (Glycine hispida)
(10)
1a
PLAT-1jnqA01
A:58-162
Clan
:
no clan defined [family: Lipoxygenase]
(13)
Family
:
Lipoxygenase
(13)
Glycine max (Soybean) (Glycine hispida)
(10)
2a
Lipoxygenase-1jnqA02
A:173-841
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Asymmetric Unit 1
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