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2YFL
Biol. Unit 2
Info
Asym.Unit (1.2 MB)
Biol.Unit 1 (643 KB)
Biol.Unit 2 (618 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BIPHENYL DIOXYGENASE VARIANT RR41 WITH 2-CHLORO DIBENZOFURAN
Authors
:
P. Kumar, J. T. Bolin
Date
:
06 Apr 11 (Deposition) - 16 May 12 (Release) - 30 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: G,H,I,J,K,L (1x)
Biol. Unit 2: A,B,C,D,E,F (1x)
Keywords
:
Oxidoreductase, Degradation, Bpdo
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
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Reference
:
P. Kumar, M. Mohammadi, S. Dhindwal, T. T. Pham, J. T. Bolin, M. Sylvestre
Structural Insights Into The Metabolism Of 2- Chlorodibenzofuran By An Evolved Biphenyl Dioxygenase.
Biochem. Biophys. Res. Commun. V. 421 757 2012
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: 2-CHLORODIBENZOFURAN (DC4a)
1b: 2-CHLORODIBENZOFURAN (DC4b)
2a: FE (II) ION (FE2a)
2b: FE (II) ION (FE2b)
2c: FE (II) ION (FE2c)
2d: FE (II) ION (FE2d)
2e: FE (II) ION (FE2e)
2f: FE (II) ION (FE2f)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
3e: FE2/S2 (INORGANIC) CLUSTER (FESe)
3f: FE2/S2 (INORGANIC) CLUSTER (FESf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DC4
2
Ligand/Ion
2-CHLORODIBENZOFURAN
2
FE2
3
Ligand/Ion
FE (II) ION
3
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:100 , HIS A:102 , ARG A:103 , CYS A:120 , HIS A:123 , TRP A:125
BINDING SITE FOR RESIDUE FES A 900
2
AC2
SOFTWARE
GLN A:226 , HIS A:233 , HIS A:239 , ASP A:388 , HOH A:2030
BINDING SITE FOR RESIDUE FE2 A 901
3
AC3
SOFTWARE
GLN A:226 , ASP A:230 , MET A:231 , HIS A:233 , SER A:283 , HIS A:323 , LEU A:333 , HOH A:2030 , HOH A:2042
BINDING SITE FOR RESIDUE DC4 A1460
4
AC4
SOFTWARE
CYS C:100 , HIS C:102 , ARG C:103 , CYS C:120 , HIS C:123 , TRP C:125
BINDING SITE FOR RESIDUE FES C 900
5
AC5
SOFTWARE
GLN C:226 , HIS C:233 , HIS C:239 , ASP C:388 , DC4 C:1460 , HOH C:2027
BINDING SITE FOR RESIDUE FE2 C 901
6
AC6
SOFTWARE
GLN C:226 , PHE C:227 , ASP C:230 , MET C:231 , HIS C:233 , HIS C:323 , PHE C:378 , PHE C:384 , ASP C:388 , FE2 C:901 , HOH C:2027
BINDING SITE FOR RESIDUE DC4 C1460
7
AC7
SOFTWARE
CYS E:100 , HIS E:102 , ARG E:103 , MET E:105 , CYS E:120 , HIS E:123 , TRP E:125
BINDING SITE FOR RESIDUE FES E 900
8
AC8
SOFTWARE
GLN E:226 , HIS E:233 , HIS E:239 , ASP E:388 , HOH E:2035
BINDING SITE FOR RESIDUE FE2 E 901
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: RIESKE (A:58-140,C:58-140,E:58-140)
2: RING_HYDROXYL_ALPHA (A:100-123,C:100-123,E:100-123)
;
View:
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
BPHA_PARXL
58-140
3
A:58-140
C:58-140
E:58-140
-
-
-
2
RING_HYDROXYL_ALPHA
PS00570
Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
BPHA_PARXL
100-123
3
A:100-123
C:100-123
E:100-123
-
-
-
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Exons
(0, 0)
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Note:
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
(3, 18)
Info
All SCOP Domains
1a: SCOP_d2yfla1 (A:18-179)
1b: SCOP_d2yflc1 (C:18-179)
1c: SCOP_d2yfle1 (E:18-179)
1d: SCOP_d2yflg1 (G:18-179)
1e: SCOP_d2yfli1 (I:18-179)
1f: SCOP_d2yflk1 (K:18-179)
2a: SCOP_d2yflb_ (B:)
2b: SCOP_d2yfld_ (D:)
2c: SCOP_d2yflf_ (F:)
2d: SCOP_d2yflh_ (H:)
2e: SCOP_d2yflj_ (J:)
2f: SCOP_d2yfll_ (L:)
3a: SCOP_d2yfla2 (A:180-459)
3b: SCOP_d2yflc2 (C:180-459)
3c: SCOP_d2yfle2 (E:180-459)
3d: SCOP_d2yflg2 (G:180-459)
3e: SCOP_d2yfli2 (I:180-459)
3f: SCOP_d2yflk2 (K:180-459)
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)
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Protein Domains
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Organisms
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Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
automated matches
(22)
Protein domain
:
automated matches
(22)
Burkholderia xenovorans [TaxId: 266265]
(7)
1a
d2yfla1
A:18-179
1b
d2yflc1
C:18-179
1c
d2yfle1
E:18-179
1d
d2yflg1
G:18-179
1e
d2yfli1
I:18-179
1f
d2yflk1
K:18-179
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
NTF2-like
(231)
Family
:
Ring hydroxylating beta subunit
(46)
Protein domain
:
automated matches
(12)
Burkholderia xenovorans [TaxId: 266265]
(7)
2a
d2yflb_
B:
2b
d2yfld_
D:
2c
d2yflf_
F:
2d
d2yflh_
H:
2e
d2yflj_
J:
2f
d2yfll_
L:
Fold
:
TBP-like
(289)
Superfamily
:
Bet v1-like
(158)
Family
:
automated matches
(39)
Protein domain
:
automated matches
(39)
Burkholderia xenovorans [TaxId: 266265]
(7)
3a
d2yfla2
A:180-459
3b
d2yflc2
C:180-459
3c
d2yfle2
E:180-459
3d
d2yflg2
G:180-459
3e
d2yfli2
I:180-459
3f
d2yflk2
K:180-459
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Sorry, no Info available
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (1.2 MB)
Header - Asym.Unit
Biol.Unit 1 (643 KB)
Header - Biol.Unit 1
Biol.Unit 2 (618 KB)
Header - Biol.Unit 2
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