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1YKN
Asym. Unit
Info
Asym.Unit (458 KB)
Biol.Unit 1 (888 KB)
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(1)
Title
:
PROTOCATECHUATE 3,4-DIOXYGENASE Y408E MUTANT BOUND TO DHB
Authors
:
C. K. Brown, D. H. Ohlendorf
Date
:
18 Jan 05 (Deposition) - 16 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.06
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (2x)
Keywords
:
Catechol, Protocatechuate, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. P. Valley, C. K. Brown, D. L. Burk, M. W. Vetting, D. H. Ohlendorf, J. D. Lipscomb
Roles Of The Equatorial Tyrosyl Iron Ligand Of Protocatechuate 3, 4-Dioxygenase In Catalysis
Biochemistry V. 44 11024 2005
[
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Hetero Components
(3, 18)
Info
All Hetero Components
1a: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEa)
1b: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEb)
1c: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEc)
1d: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEd)
1e: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEe)
1f: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEf)
2a: 3,4-DIHYDROXYBENZOIC ACID (DHBa)
2b: 3,4-DIHYDROXYBENZOIC ACID (DHBb)
2c: 3,4-DIHYDROXYBENZOIC ACID (DHBc)
2d: 3,4-DIHYDROXYBENZOIC ACID (DHBd)
2e: 3,4-DIHYDROXYBENZOIC ACID (DHBe)
2f: 3,4-DIHYDROXYBENZOIC ACID (DHBf)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
3e: FE (III) ION (FEe)
3f: FE (III) ION (FEf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CME
6
Mod. Amino Acid
S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2
DHB
6
Ligand/Ion
3,4-DIHYDROXYBENZOIC ACID
3
FE
6
Ligand/Ion
FE (III) ION
[
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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: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR B:447 , HIS B:460 , HIS B:462 , DHB B:550 , HOH B:901
BINDING SITE FOR RESIDUE FE B 600
02
AC2
SOFTWARE
TYR D:447 , HIS D:460 , HIS D:462 , DHB D:1550 , HOH D:1901
BINDING SITE FOR RESIDUE FE D 1600
03
AC3
SOFTWARE
TYR F:447 , HIS F:460 , HIS F:462 , DHB F:2550 , HOH F:2901
BINDING SITE FOR RESIDUE FE F 2600
04
AC4
SOFTWARE
TYR H:447 , HIS H:460 , HIS H:462 , DHB H:3550 , HOH H:3901
BINDING SITE FOR RESIDUE FE H 3600
05
AC5
SOFTWARE
GLU J:408 , TYR J:447 , HIS J:460 , HIS J:462 , DHB J:4550 , HOH J:4901
BINDING SITE FOR RESIDUE FE J 4600
06
AC6
SOFTWARE
TYR L:447 , HIS L:460 , HIS L:462 , DHB L:5550 , HOH L:5901
BINDING SITE FOR RESIDUE FE L 5600
07
AC7
SOFTWARE
THR A:12 , GLY A:14 , PRO A:15 , ARG A:133 , TYR B:324 , TYR B:447 , TRP B:449 , ARG B:457 , HIS B:460 , GLN B:477 , ILE B:491 , FE B:600 , HOH B:678
BINDING SITE FOR RESIDUE DHB B 550
08
AC8
SOFTWARE
GLY C:14 , PRO C:15 , ARG C:133 , TYR D:324 , TYR D:447 , TRP D:449 , ARG D:457 , HIS D:460 , HIS D:462 , GLN D:477 , ILE D:491 , FE D:1600 , HOH D:1678
BINDING SITE FOR RESIDUE DHB D 1550
09
AC9
SOFTWARE
GLY E:14 , PRO E:15 , ARG E:133 , TYR F:324 , TYR F:447 , TRP F:449 , ARG F:457 , HIS F:460 , HIS F:462 , GLN F:477 , FE F:2600 , HOH F:2678
BINDING SITE FOR RESIDUE DHB F 2550
10
BC1
SOFTWARE
THR G:12 , GLY G:14 , PRO G:15 , ARG G:133 , TYR H:324 , TYR H:447 , TRP H:449 , ARG H:457 , HIS H:460 , HIS H:462 , GLN H:477 , FE H:3600 , HOH H:3678
BINDING SITE FOR RESIDUE DHB H 3550
11
BC2
SOFTWARE
THR I:12 , GLY I:14 , PRO I:15 , ARG I:133 , TYR J:324 , TYR J:447 , TRP J:449 , ARG J:457 , HIS J:460 , HIS J:462 , GLN J:477 , ILE J:491 , FE J:4600 , HOH J:4678
BINDING SITE FOR RESIDUE DHB J 4550
12
BC3
SOFTWARE
THR K:12 , GLY K:14 , PRO K:15 , ARG K:133 , TYR L:324 , TYR L:447 , TRP L:449 , ARG L:457 , HIS L:460 , HIS L:462 , GLN L:477 , ILE L:491 , FE L:5600 , HOH L:5678
BINDING SITE FOR RESIDUE DHB L 5550
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 12)
Info
All PROSITE Patterns/Profiles
1: INTRADIOL_DIOXYGENAS (A:51-79,C:51-79,E:51-79,G:51-79,I:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTRADIOL_DIOXYGENAS
PS00083
Intradiol ring-cleavage dioxygenases signature.
PCXA_PSEPU
52-80
6
A:51-79
C:51-79
E:51-79
G:51-79
I:51-79
K:51-79
PCXB_PSEPU
81-109
6
B:380-407
D:380-407
F:380-407
H:380-407
J:380-407
L:380-407
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1ykna_ (A:)
1b: SCOP_d1yknc_ (C:)
1c: SCOP_d1ykne_ (E:)
1d: SCOP_d1ykng_ (G:)
1e: SCOP_d1ykni_ (I:)
1f: SCOP_d1yknk_ (K:)
2a: SCOP_d1yknb_ (B:)
2b: SCOP_d1yknd_ (D:)
2c: SCOP_d1yknf_ (F:)
2d: SCOP_d1yknh_ (H:)
2e: SCOP_d1yknj_ (J:)
2f: SCOP_d1yknl_ (L:)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Prealbumin-like
(433)
Superfamily
:
Aromatic compound dioxygenase
(111)
Family
:
Aromatic compound dioxygenase
(100)
Protein domain
:
Protocatechuate-3,4-dioxygenase, alpha chain
(37)
Pseudomonas putida [TaxId: 303]
(31)
1a
d1ykna_
A:
1b
d1yknc_
C:
1c
d1ykne_
E:
1d
d1ykng_
G:
1e
d1ykni_
I:
1f
d1yknk_
K:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d1yknb_
B:
2b
d1yknd_
D:
2c
d1yknf_
F:
2d
d1yknh_
H:
2e
d1yknj_
J:
2f
d1yknl_
L:
[
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1yknB00 (B:301-538)
1b: CATH_1yknA00 (A:1-200)
1c: CATH_1yknC00 (C:1-200)
1d: CATH_1yknE00 (E:1-200)
1e: CATH_1yknG00 (G:1-200)
1f: CATH_1yknI00 (I:1-200)
1g: CATH_1yknK00 (K:1-200)
1h: CATH_1yknD00 (D:301-538)
1i: CATH_1yknF00 (F:301-538)
1j: CATH_1yknH00 (H:301-538)
1k: CATH_1yknJ00 (J:301-538)
1l: CATH_1yknL00 (L:301-538)
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)
(
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Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Protocatechuate 3,4-Dioxygenase, subunit A
(43)
Homologous Superfamily
:
Protocatechuate 3,4-Dioxygenase, subunit A
(43)
Pseudomonas putida. Organism_taxid: 303.
(20)
1a
1yknB00
B:301-538
1b
1yknA00
A:1-200
1c
1yknC00
C:1-200
1d
1yknE00
E:1-200
1e
1yknG00
G:1-200
1f
1yknI00
I:1-200
1g
1yknK00
K:1-200
1h
1yknD00
D:301-538
1i
1yknF00
F:301-538
1j
1yknH00
H:301-538
1k
1yknJ00
J:301-538
1l
1yknL00
L:301-538
[
close CATH info
]
Pfam Domains
(2, 18)
Info
all PFAM domains
1a: PFAM_Dioxygenase_C_1yknK01 (K:23-192)
1b: PFAM_Dioxygenase_C_1yknK02 (K:23-192)
1c: PFAM_Dioxygenase_C_1yknK03 (K:23-192)
1d: PFAM_Dioxygenase_C_1yknK04 (K:23-192)
1e: PFAM_Dioxygenase_C_1yknK05 (K:23-192)
1f: PFAM_Dioxygenase_C_1yknK06 (K:23-192)
1g: PFAM_Dioxygenase_C_1yknL01 (L:346-530)
1h: PFAM_Dioxygenase_C_1yknL02 (L:346-530)
1i: PFAM_Dioxygenase_C_1yknL03 (L:346-530)
1j: PFAM_Dioxygenase_C_1yknL04 (L:346-530)
1k: PFAM_Dioxygenase_C_1yknL05 (L:346-530)
1l: PFAM_Dioxygenase_C_1yknL06 (L:346-530)
2a: PFAM_PCDO_beta_N_1yknL07 (L:308-343)
2b: PFAM_PCDO_beta_N_1yknL08 (L:308-343)
2c: PFAM_PCDO_beta_N_1yknL09 (L:308-343)
2d: PFAM_PCDO_beta_N_1yknL10 (L:308-343)
2e: PFAM_PCDO_beta_N_1yknL11 (L:308-343)
2f: PFAM_PCDO_beta_N_1yknL12 (L:308-343)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Transthyretin
(88)
Family
:
Dioxygenase_C
(32)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(27)
1a
Dioxygenase_C-1yknK01
K:23-192
1b
Dioxygenase_C-1yknK02
K:23-192
1c
Dioxygenase_C-1yknK03
K:23-192
1d
Dioxygenase_C-1yknK04
K:23-192
1e
Dioxygenase_C-1yknK05
K:23-192
1f
Dioxygenase_C-1yknK06
K:23-192
1g
Dioxygenase_C-1yknL01
L:346-530
1h
Dioxygenase_C-1yknL02
L:346-530
1i
Dioxygenase_C-1yknL03
L:346-530
1j
Dioxygenase_C-1yknL04
L:346-530
1k
Dioxygenase_C-1yknL05
L:346-530
1l
Dioxygenase_C-1yknL06
L:346-530
Clan
:
no clan defined [family: PCDO_beta_N]
(26)
Family
:
PCDO_beta_N
(26)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(26)
2a
PCDO_beta_N-1yknL07
L:308-343
2b
PCDO_beta_N-1yknL08
L:308-343
2c
PCDO_beta_N-1yknL09
L:308-343
2d
PCDO_beta_N-1yknL10
L:308-343
2e
PCDO_beta_N-1yknL11
L:308-343
2f
PCDO_beta_N-1yknL12
L:308-343
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