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1IK3
Asym. Unit
Info
Asym.Unit (156 KB)
Biol.Unit 1 (149 KB)
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(1)
Title
:
LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
Authors
:
E. Skrzypczak-Jankun, M. O. Funk Jr.
Date
:
01 May 01 (Deposition) - 14 Nov 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Oxidoreductase, Purple Lipoxygenase, Fe(Iii) Complex, Interm
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Skrzypczak-Jankun, R. A. Bross, R. T. Carroll, W. R. Dunham, M. O. Funk
Three-Dimensional Structure Of A Purple Lipoxygenase.
J. Am. Chem. Soc. V. 123 10814 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 5)
Info
All Hetero Components
1a: (TRANS-12,13-EPOXY)-11-HYDROXY-9(Z... (11Oa)
2a: 13(R)-HYDROPEROXY-9(Z),11(E)-OCTAD... (13Ra)
3a: 13(S)-HYDROPEROXY-9(Z),11(E)-OCTAD... (13Sa)
4a: (TRANS-12,13-EPOXY)-9-HYDROXY-10(E... (9OHa)
5a: FE (III) ION (FEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
11O
1
Ligand/Ion
(TRANS-12,13-EPOXY)-11-HYDROXY-9(Z)-OCTADECENOIC ACID
2
13R
1
Ligand/Ion
13(R)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
3
13S
1
Ligand/Ion
13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
4
9OH
1
Ligand/Ion
(TRANS-12,13-EPOXY)-9-HYDROXY-10(E)-OCTADECENOIC ACID
5
FE
1
Ligand/Ion
FE (III) ION
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: FE3 (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:518 , HIS A:523 , HIS A:709 , ASN A:713 , ILE A:857 , 13S A:1859
BINDING SITE FOR RESIDUE FE A 858
2
AC2
SOFTWARE
LEU A:273 , LEU A:277 , VAL A:372 , SER A:510 , HIS A:513 , GLN A:514 , HIS A:518 , HIS A:523 , ILE A:557 , LEU A:560 , LEU A:565 , PHE A:576 , ASN A:713 , GLN A:716 , ARG A:726 , LEU A:773 , ILE A:857 , FE A:858
BINDING SITE FOR RESIDUE 13S A 1859
3
FE3
AUTHOR
FE A:858 , HIS A:518 , HIS A:523 , HIS A:709 , ILE A:857 , 13S A:1859
IRON (FE+3) ACTIVE SITE
[
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SAPs(SNPs)/Variants
(7, 7)
Info
(mutated residues are not available)
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:46-163)
2: LIPOXYGENASE_3 (A:166-857)
3: LIPOXYGENASE_1 (A:513-527)
4: LIPOXYGENASE_2 (A:540-550)
;
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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:46-163
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
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1ik3a1 (A:168-857)
2a: SCOP_d1ik3a2 (A:9-167)
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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
d1ik3a1
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
d1ik3a2
A:9-167
[
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CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1ik3A04 (A:357-490)
2a: CATH_1ik3A02 (A:168-267)
3a: CATH_1ik3A03 (A:268-356)
4a: CATH_1ik3A05 (A:491-856)
5a: CATH_1ik3A01 (A:9-167)
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Organisms
(
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(
)
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
1ik3A04
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
1ik3A02
A:168-267
Topology
:
Lipoxygenase-1; domain 3
(24)
Homologous Superfamily
:
Lipoxygenase-1; Domain 3
(24)
Soybean (Glycine max)
(24)
3a
1ik3A03
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
1ik3A05
A:491-856
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Lipoxygenase-1
(46)
Homologous Superfamily
:
Lipoxygenase-1
(44)
Soybean (Glycine max)
(24)
5a
1ik3A01
A:9-167
[
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Pfam Domains
(0, 0)
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