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2B1X
Asym. Unit
Info
Asym.Unit (326 KB)
Biol.Unit 1 (317 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NAPHTHALENE 1,2-DIOXYGENASE FROM RHODOCOCCUS SP.
Authors
:
L. Gakhar, Z. A. Malik, C. C. Allen, D. A. Lipscomb, M. J. Larkin, S. Ramas
Date
:
16 Sep 05 (Deposition) - 04 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Rieske Non-Heme Iron Oxygenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
L. Gakhar, Z. A. Malik, C. C. Allen, D. A. Lipscomb, M. J. Larkin, S. Ramaswamy
Structure And Increased Thermostability Of Rhodococcus Sp. Naphthalene 1, 2-Dioxygenase.
J. Bacteriol. V. 187 7222 2005
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Hetero Components
(3, 19)
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)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
3e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
3f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
3g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
3h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
3i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
3j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
3k: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDk)
3l: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDl)
3m: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDm)
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
3
MPD
13
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
[
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Sites
(19, 19)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:216 , HIS A:221 , ASP A:372 , HOH A:1961 , HOH A:1962
BINDING SITE FOR RESIDUE FE A 502
02
AC2
SOFTWARE
HIS C:216 , HIS C:221 , ASP C:372 , HOH C:1957 , HOH C:1958
BINDING SITE FOR RESIDUE FE C 502
03
AC3
SOFTWARE
HIS E:216 , HIS E:221 , ASP E:372 , HOH E:2010 , HOH E:2011
BINDING SITE FOR RESIDUE FE E 502
04
AC4
SOFTWARE
CYS A:88 , HIS A:90 , ARG A:91 , CYS A:108 , HIS A:111 , GLY A:112 , TRP A:113
BINDING SITE FOR RESIDUE FES A 501
05
AC5
SOFTWARE
CYS C:88 , HIS C:90 , ARG C:91 , CYS C:108 , TYR C:110 , HIS C:111 , TRP C:113
BINDING SITE FOR RESIDUE FES C 501
06
AC6
SOFTWARE
CYS E:88 , HIS E:90 , ARG E:91 , CYS E:108 , HIS E:111 , TRP E:113
BINDING SITE FOR RESIDUE FES E 501
07
AC7
SOFTWARE
ASP A:213 , HIS A:216 , THR A:217 , HIS A:221 , HIS A:295 , PHE A:362 , HOH A:1962
BINDING SITE FOR RESIDUE MPD A 1700
08
AC8
SOFTWARE
ARG A:222 , ARG C:107 , PRO C:125
BINDING SITE FOR RESIDUE MPD C 1701
09
AC9
SOFTWARE
GLU A:226
BINDING SITE FOR RESIDUE MPD A 1702
10
BC1
SOFTWARE
GLU A:374 , ARG A:377 , ARG A:381 , ARG B:632 , GLY B:633 , VAL B:635 , GLN C:94
BINDING SITE FOR RESIDUE MPD A 1703
11
BC2
SOFTWARE
ASP C:213 , ALA C:214 , HIS C:216 , THR C:217 , HIS C:295 , HOH C:1958
BINDING SITE FOR RESIDUE MPD C 1704
12
BC3
SOFTWARE
MET C:218 , ARG C:222 , ARG E:107
BINDING SITE FOR RESIDUE MPD E 1705
13
BC4
SOFTWARE
GLU C:374 , ARG C:377 , ARG C:381 , ARG D:632 , GLY D:633 , VAL D:635 , GLN E:94
BINDING SITE FOR RESIDUE MPD C 1707
14
BC5
SOFTWARE
ASP E:213 , ALA E:214 , HIS E:216 , THR E:217 , HIS E:295 , HOH E:2010
BINDING SITE FOR RESIDUE MPD E 1708
15
BC6
SOFTWARE
ARG A:107 , ARG E:222
BINDING SITE FOR RESIDUE MPD A 1709
16
BC7
SOFTWARE
VAL E:225
BINDING SITE FOR RESIDUE MPD E 1710
17
BC8
SOFTWARE
GLN A:94 , GLU E:374 , ARG E:377 , SER E:378 , ARG E:381 , ARG F:632 , GLY F:633
BINDING SITE FOR RESIDUE MPD E 1711
18
BC9
SOFTWARE
PRO E:231 , MET E:260 , PHE E:293 , HOH E:1778 , HOH E:1838
BINDING SITE FOR RESIDUE MPD E 1712
19
CC1
SOFTWARE
TYR E:61 , VAL E:95 , CYS E:96 , ARG E:97 , ALA E:98 , HOH E:1807 , HOH E:1911 , GLU F:560
BINDING SITE FOR RESIDUE MPD E 1713
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 9)
Info
All SCOP Domains
1a: SCOP_d2b1xa1 (A:1-162)
1b: SCOP_d2b1xc1 (C:1-162)
1c: SCOP_d2b1xe1 (E:1-162)
2a: SCOP_d2b1xd_ (D:)
2b: SCOP_d2b1xf_ (F:)
3a: SCOP_d2b1xb1 (B:513-679)
4a: SCOP_d2b1xa2 (A:163-441)
4b: SCOP_d2b1xc2 (C:163-441)
4c: SCOP_d2b1xe2 (E:163-441)
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(
)
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)
Rhodococcus sp. ncimb12038 [TaxId: 92694]
(1)
1a
d2b1xa1
A:1-162
1b
d2b1xc1
C:1-162
1c
d2b1xe1
E:1-162
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
NTF2-like
(231)
Family
:
automated matches
(27)
Protein domain
:
automated matches
(27)
Rhodococcus sp. [TaxId: 92694]
(1)
2a
d2b1xd_
D:
2b
d2b1xf_
F:
Family
:
Ring hydroxylating beta subunit
(46)
Protein domain
:
Naphthalene 1,2-dioxygenase beta subunit
(28)
Rhodococcus sp. ncimb12038 [TaxId: 92694]
(1)
3a
d2b1xb1
B:513-679
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)
Rhodococcus sp. ncimb12038 [TaxId: 92694]
(1)
4a
d2b1xa2
A:163-441
4b
d2b1xc2
C:163-441
4c
d2b1xe2
E:163-441
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2b1xA02 (A:45-170)
1b: CATH_2b1xC02 (C:45-170)
1c: CATH_2b1xE02 (E:45-170)
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Organisms
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)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Ncimb12038 (Rhodococcus sp)
(2)
1a
2b1xA02
A:45-170
1b
2b1xC02
C:45-170
1c
2b1xE02
E:45-170
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Sorry, no Info available
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Protein & NOT PROSITE
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Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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