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1NDO
Asym. Unit
Info
Asym.Unit (334 KB)
Biol.Unit 1 (328 KB)
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(1)
Title
:
NAPTHALENE 1,2-DIOXYGENASE
Authors
:
S. Ramaswamy, B. Kauppi, E. Carredano
Date
:
11 Jan 98 (Deposition) - 23 Mar 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Non-Heme Iron Dioxygenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Kauppi, K. Lee, E. Carredano, R. E. Parales, D. T. Gibson, H. Eklund, S. Ramaswamy
Structure Of An Aromatic-Ring-Hydroxylating Dioxygenase-Naphthalene 1, 2-Dioxygenase.
Structure V. 6 571 1998
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 6)
Info
All Hetero Components
2a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2b: FE2/S2 (INORGANIC) CLUSTER (FESb)
2c: FE2/S2 (INORGANIC) CLUSTER (FESc)
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
3
Ligand/Ion
FE (III) ION
2
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: MO1 (UNKNOWN)
08: MO2 (UNKNOWN)
09: MO3 (UNKNOWN)
10: RK1 (UNKNOWN)
11: RK2 (UNKNOWN)
12: RK3 (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:208 , HIS A:213 , ASP A:362
BINDING SITE FOR RESIDUE FE A 452
02
AC2
SOFTWARE
ASN C:201 , HIS C:208 , HIS C:213 , ASP C:362
BINDING SITE FOR RESIDUE FE C 452
03
AC3
SOFTWARE
HIS E:208 , HIS E:213 , ASP E:362
BINDING SITE FOR RESIDUE FE E 452
04
AC4
SOFTWARE
CYS A:81 , HIS A:83 , ARG A:84 , CYS A:101 , TYR A:103 , HIS A:104 , TRP A:106
BINDING SITE FOR RESIDUE FES A 451
05
AC5
SOFTWARE
CYS C:81 , HIS C:83 , ARG C:84 , CYS C:101 , TYR C:103 , HIS C:104 , TRP C:106
BINDING SITE FOR RESIDUE FES C 451
06
AC6
SOFTWARE
CYS E:81 , HIS E:83 , ARG E:84 , CYS E:101 , TYR E:103 , HIS E:104 , TRP E:106
BINDING SITE FOR RESIDUE FES E 451
07
MO1
UNKNOWN
HIS A:213 , HIS A:208 , ASP A:362
MONO IRON SITE - THERE IS ALSO A WATER.
08
MO2
UNKNOWN
HIS C:213 , HIS C:208 , ASP C:362
MONO IRON SITE - THERE IS ALSO A WATER.
09
MO3
UNKNOWN
HIS E:213 , HIS E:208 , ASP E:362
MONO IRON SITE - THERE IS ALSO A WATER.
10
RK1
UNKNOWN
CYS A:81 , CYS A:101 , HIS A:83 , HIS C:104
RIESKE CENTER - FIRST TWO ARE LIGANDS TO FE1 AND THE NEXT TO FE2.
11
RK2
UNKNOWN
CYS C:81 , CYS C:101 , HIS C:83 , HIS C:104
RIESKE CENTER - FIRST TWO ARE LIGANDS TO FE1 AND THE NEXT TO FE2.
12
RK3
UNKNOWN
CYS E:81 , CYS E:101 , HIS E:83 , HIS E:104
RIESKE CENTER - FIRST TWO ARE LIGANDS TO FE1 AND THE NEXT TO FE2.
[
close Site info
]
SAPs(SNPs)/Variants
(23, 69)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_NDOB_PSEPU_001 (N4K, chain A/C/E, )
02: VAR_NDOB_PSEPU_002 (S12F, chain A/C/E, )
03: VAR_NDOB_PSEPU_003 (S15T, chain A/C/E, )
04: VAR_NDOB_PSEPU_004 (K32R, chain A/C/E, )
05: VAR_NDOB_PSEPU_005 (A50S, chain A/C/E, )
06: VAR_NDOB_PSEPU_006 (N70S, chain A/C/E, )
07: VAR_NDOB_PSEPU_007 (D122E, chain A/C/E, )
08: VAR_NDOB_PSEPU_008 (M173I, chain A/C/E, )
09: VAR_NDOB_PSEPU_009 (S225A, chain A/C/E, )
10: VAR_NDOB_PSEPU_010 (S225C, chain A/C/E, )
11: VAR_NDOB_PSEPU_011 (A232V, chain A/C/E, )
12: VAR_NDOB_PSEPU_012 (A275S, chain A/C/E, )
13: VAR_NDOB_PSEPU_013 (E391K, chain A/C/E, )
14: VAR_NDOB_PSEPU_014 (Q421R, chain A/C/E, )
15: VAR_NDOB_PSEPU_015 (H434D, chain A/C/E, )
16: VAR_NDOC_PSEPU_001 (E517Q, chain B/D/F, )
17: VAR_NDOC_PSEPU_002 (I519F, chain B/D/F, )
18: VAR_NDOC_PSEPU_003 (S528A, chain B/D/F, )
19: VAR_NDOC_PSEPU_004 (V599I, chain B/D/F, )
20: VAR_NDOC_PSEPU_005 (G609S, chain B/D/F, )
21: VAR_NDOC_PSEPU_006 (M627R, chain B/D/F, )
22: VAR_NDOC_PSEPU_007 (N630D, chain B/D/F, )
23: VAR_NDOC_PSEPU_008 (K632E, chain B/D/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_NDOB_PSEPU_001
*
N
4
K
NDOB_PSEPU
---
---
A/C/E
N
4
K
02
UniProt
VAR_NDOB_PSEPU_002
*
S
12
F
NDOB_PSEPU
---
---
A/C/E
S
12
F
03
UniProt
VAR_NDOB_PSEPU_003
*
S
15
T
NDOB_PSEPU
---
---
A/C/E
S
15
T
04
UniProt
VAR_NDOB_PSEPU_004
*
K
32
R
NDOB_PSEPU
---
---
A/C/E
K
32
R
05
UniProt
VAR_NDOB_PSEPU_005
*
A
50
S
NDOB_PSEPU
---
---
A/C/E
A
50
S
06
UniProt
VAR_NDOB_PSEPU_006
*
N
70
S
NDOB_PSEPU
---
---
A/C/E
N
70
S
07
UniProt
VAR_NDOB_PSEPU_007
*
D
122
E
NDOB_PSEPU
---
---
A/C/E
D
122
E
08
UniProt
VAR_NDOB_PSEPU_008
*
M
173
I
NDOB_PSEPU
---
---
A/C/E
M
173
I
09
UniProt
VAR_NDOB_PSEPU_009
*
S
225
A
NDOB_PSEPU
---
---
A/C/E
S
225
A
10
UniProt
VAR_NDOB_PSEPU_010
*
S
225
C
NDOB_PSEPU
---
---
A/C/E
S
225
C
11
UniProt
VAR_NDOB_PSEPU_011
*
A
232
V
NDOB_PSEPU
---
---
A/C/E
A
232
V
12
UniProt
VAR_NDOB_PSEPU_012
*
A
275
S
NDOB_PSEPU
---
---
A/C/E
A
275
S
13
UniProt
VAR_NDOB_PSEPU_013
*
E
391
K
NDOB_PSEPU
---
---
A/C/E
E
391
K
14
UniProt
VAR_NDOB_PSEPU_014
*
Q
421
R
NDOB_PSEPU
---
---
A/C/E
Q
421
R
15
UniProt
VAR_NDOB_PSEPU_015
*
H
434
D
NDOB_PSEPU
---
---
A/C/E
H
434
D
16
UniProt
VAR_NDOC_PSEPU_001
*
E
17
Q
NDOC_PSEPU
---
---
B/D/F
E
517
Q
17
UniProt
VAR_NDOC_PSEPU_002
*
I
19
F
NDOC_PSEPU
---
---
B/D/F
I
519
F
18
UniProt
VAR_NDOC_PSEPU_003
*
S
28
A
NDOC_PSEPU
---
---
B/D/F
S
528
A
19
UniProt
VAR_NDOC_PSEPU_004
*
V
99
I
NDOC_PSEPU
---
---
B/D/F
V
599
I
20
UniProt
VAR_NDOC_PSEPU_005
*
G
109
S
NDOC_PSEPU
---
---
B/D/F
G
609
S
21
UniProt
VAR_NDOC_PSEPU_006
*
M
127
R
NDOC_PSEPU
---
---
B/D/F
M
627
R
22
UniProt
VAR_NDOC_PSEPU_007
*
N
130
D
NDOC_PSEPU
---
---
B/D/F
N
630
D
23
UniProt
VAR_NDOC_PSEPU_008
*
K
132
E
NDOC_PSEPU
---
---
B/D/F
K
632
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: RIESKE (A:39-123,C:39-123,E:39-123)
2: RING_HYDROXYL_ALPHA (A:81-104,C:81-104,E:81-104)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
NDOB_PSEPU
39-123
3
A:39-123
C:39-123
E:39-123
2
RING_HYDROXYL_ALPHA
PS00570
Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
NDOB_PSEPU
81-104
3
A:81-104
C:81-104
E:81-104
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 9)
Info
All SCOP Domains
1a: SCOP_d1ndoa1 (A:1-154)
1b: SCOP_d1ndoc1 (C:1-154)
1c: SCOP_d1ndoe1 (E:1-154)
2a: SCOP_d1ndob_ (B:)
2b: SCOP_d1ndod_ (D:)
2c: SCOP_d1ndof_ (F:)
3a: SCOP_d1ndoa2 (A:155-447)
3b: SCOP_d1ndoc2 (C:155-447)
3c: SCOP_d1ndoe2 (E:155-445)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Ring hydroxylating alpha subunit ISP domain
(40)
Protein domain
:
Naphthalene 1,2-dioxygenase alpha subunit, N-domain
(27)
Pseudomonas putida [TaxId: 303]
(10)
1a
d1ndoa1
A:1-154
1b
d1ndoc1
C:1-154
1c
d1ndoe1
E:1-154
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
NTF2-like
(231)
Family
:
Ring hydroxylating beta subunit
(46)
Protein domain
:
Naphthalene 1,2-dioxygenase beta subunit
(28)
Pseudomonas putida [TaxId: 303]
(10)
2a
d1ndob_
B:
2b
d1ndod_
D:
2c
d1ndof_
F:
Fold
:
TBP-like
(289)
Superfamily
:
Bet v1-like
(158)
Family
:
Ring hydroxylating alpha subunit catalytic domain
(42)
Protein domain
:
Naphthalene 1,2-dioxygenase alpha subunit, C-domain
(29)
Pseudomonas putida [TaxId: 303]
(10)
3a
d1ndoa2
A:155-447
3b
d1ndoc2
C:155-447
3c
d1ndoe2
E:155-445
[
close SCOP info
]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_1ndoE01 (E:1-35,E:165-445)
1b: CATH_1ndoA01 (A:1-35,A:165-447)
1c: CATH_1ndoC01 (C:1-35,C:165-447)
2a: CATH_1ndoB00 (B:502-694)
2b: CATH_1ndoD00 (D:502-694)
2c: CATH_1ndoF00 (F:502-694)
3a: CATH_1ndoA02 (A:36-164)
3b: CATH_1ndoC02 (C:36-164)
3c: CATH_1ndoE02 (E:36-164)
View:
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(
)
(
)
Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
(24)
Homologous Superfamily
:
Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
(24)
Pseudomonas putida. Organism_taxid: 303.
(1)
1a
1ndoE01
E:1-35,E:165-445
1b
1ndoA01
A:1-35,A:165-447
1c
1ndoC01
C:1-35,C:165-447
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.50, no name defined]
(113)
Pseudomonas putida. Organism_taxid: 303.
(6)
2a
1ndoB00
B:502-694
2b
1ndoD00
D:502-694
2c
1ndoF00
F:502-694
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Pseudomonas putida. Organism_taxid: 303.
(1)
3a
1ndoA02
A:36-164
3b
1ndoC02
C:36-164
3c
1ndoE02
E:36-164
[
close CATH info
]
Pfam Domains
(3, 9)
Info
all PFAM domains
1a: PFAM_Ring_hydroxyl_A_1ndoE01 (E:159-426)
1b: PFAM_Ring_hydroxyl_A_1ndoE02 (E:159-426)
1c: PFAM_Ring_hydroxyl_A_1ndoE03 (E:159-426)
2a: PFAM_Rieske_1ndoE04 (E:38-139)
2b: PFAM_Rieske_1ndoE05 (E:38-139)
2c: PFAM_Rieske_1ndoE06 (E:38-139)
3a: PFAM_Ring_hydroxyl_B_1ndoF01 (F:540-688)
3b: PFAM_Ring_hydroxyl_B_1ndoF02 (F:540-688)
3c: PFAM_Ring_hydroxyl_B_1ndoF03 (F:540-688)
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Clans
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)
Organisms
(
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)
Clan
:
Bet_V_1_like
(93)
Family
:
Ring_hydroxyl_A
(10)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(9)
1a
Ring_hydroxyl_A-1ndoE01
E:159-426
1b
Ring_hydroxyl_A-1ndoE02
E:159-426
1c
Ring_hydroxyl_A-1ndoE03
E:159-426
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(13)
2a
Rieske-1ndoE04
E:38-139
2b
Rieske-1ndoE05
E:38-139
2c
Rieske-1ndoE06
E:38-139
Clan
:
NTF2
(66)
Family
:
Ring_hydroxyl_B
(10)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(9)
3a
Ring_hydroxyl_B-1ndoF01
F:540-688
3b
Ring_hydroxyl_B-1ndoF02
F:540-688
3c
Ring_hydroxyl_B-1ndoF03
F:540-688
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